Variant report

Variant	rs12497677
Chromosome Location	chr3:195132073-195132074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195107747..195110594-chr3:195131187..195133391,2	MCF-7	breast:
2	chr3:195131548..195133612-chr3:195139507..195142026,2	K562	blood:

Variant related genes	Relation type
ENSG00000207368	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12485302	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12485380	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12485407	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12485433	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12485787	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486241	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12486536	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486805	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487670	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487961	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488451	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488481	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12488562	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12488869	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488979	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12489090	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12489620	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489849	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12490460	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12490658	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491026	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491371	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491581	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491670	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491736	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491788	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491808	0.86[AMR][1000 genomes]
rs12491854	0.86[AMR][1000 genomes]
rs12492552	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12494564	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494759	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494773	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12494820	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495657	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496202	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496204	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496885	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497178	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12497478	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12497671	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808074	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2029707	0.86[AMR][1000 genomes]
rs2050807	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2050808	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34643420	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35419807	0.86[AMR][1000 genomes]
rs3773419	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3773420	0.90[AMR][1000 genomes]
rs41266981	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41266999	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41267003	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56211708	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60040536	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6767801	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6798243	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72499627	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72607893	0.84[AMR][1000 genomes]
rs72607894	0.90[AMR][1000 genomes]
rs72607895	0.90[AMR][1000 genomes]
rs72607896	0.90[AMR][1000 genomes]
rs72607897	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72607898	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72607899	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72607900	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72607901	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72607902	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72611103	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs755202	0.84[AMR][1000 genomes]
rs7653179	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
2	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
7	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
8	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
9	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
10	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
11	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
12	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
13	nsv878139	chr3:195058837-195158031	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv1799680	chr3:195060129-195154361	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
15	nsv878141	chr3:195065255-195158031	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1006229	chr3:195071421-195474751	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
17	esv2754364	chr3:195102703-195553690	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
18	esv2757028	chr3:195102787-195479748	Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
19	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
20	nsv878142	chr3:195109866-195143983	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
21	nsv878143	chr3:195115229-195158031	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv878144	chr3:195120090-195158031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv432513	chr3:195121072-195478861	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
24	nsv432514	chr3:195121110-195478861	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
25	nsv432515	chr3:195121110-195528226	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
26	nsv829824	chr3:195131067-195286698	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195078000-195142200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:195088600-195146800	Weak transcription	Spleen	Spleen
3	chr3:195094800-195161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:195095200-195161800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:195095800-195134200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:195106600-195137800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:195108800-195134000	Weak transcription	Placenta	Placenta
8	chr3:195109400-195144000	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:195112600-195132400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:195112600-195138000	Weak transcription	Thymus	Thymus
11	chr3:195112600-195141400	Weak transcription	Fetal Stomach	stomach
12	chr3:195115400-195134200	Weak transcription	Lung	lung
13	chr3:195115600-195132400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:195115600-195139200	Weak transcription	Psoas Muscle	Psoas
15	chr3:195116200-195143600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:195116400-195147600	Weak transcription	Fetal Intestine Small	intestine
17	chr3:195117200-195133400	Weak transcription	Liver	Liver
18	chr3:195118200-195144200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:195118800-195142200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:195123000-195132600	Weak transcription	Right Ventricle	heart
21	chr3:195123800-195146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:195125000-195132600	Weak transcription	Osteobl	bone
23	chr3:195125000-195134200	Weak transcription	Ovary	ovary
24	chr3:195125000-195147600	Weak transcription	Left Ventricle	heart
25	chr3:195126600-195139800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:195126800-195134400	Weak transcription	Esophagus	oesophagus
27	chr3:195127000-195149800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:195127400-195133600	Weak transcription	HUVEC	blood vessel
29	chr3:195128000-195132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:195128000-195134200	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:195128000-195139200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:195128600-195138000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:195129200-195132400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:195129800-195132800	Weak transcription	Fetal Brain Male	brain
35	chr3:195130000-195142000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:195130000-195142400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:195130400-195134000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:195130800-195132200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:195130800-195132600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr3:195131000-195132600	Strong transcription	Primary B cells from cord blood	blood
41	chr3:195131000-195132600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:195131000-195132800	Strong transcription	Primary T cells from cord blood	blood
43	chr3:195131000-195135000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:195131200-195132200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:195131200-195132200	Strong transcription	Fetal Lung	lung
46	chr3:195131200-195132600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:195131200-195132600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:195131200-195132800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:195131200-195132800	Strong transcription	Dnd41	blood
50	chr3:195131200-195133400	Strong transcription	Fetal Intestine Large	intestine

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