Variant report

Variant	rs12495831
Chromosome Location	chr3:49927722-49927723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49926353..49927949-chr3:49939472..49941342,2	K562	blood:
2	chr3:49927426..49930206-chr3:49934919..49938158,3	K562	blood:
3	chr3:49920847..49922840-chr3:49927620..49929225,2	K562	blood:
4	chr3:49927718..49929244-chr3:49938416..49939964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228008	Chromatin interaction
ENSG00000164078	Chromatin interaction
ENSG00000230698	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs11130223	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130225	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130239	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130240	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11717463	0.84[YRI][hapmap]
rs11916261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11920034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11923132	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11925156	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486470	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12486808	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486832	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12489386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492291	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493565	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494077	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494172	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494916	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12629129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629677	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12630917	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630959	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631309	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631608	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632751	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636045	0.87[AMR][1000 genomes]
rs12636669	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637222	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637681	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638046	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317215	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13326300	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023951	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28478136	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35333166	0.87[AMR][1000 genomes]
rs41291716	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55643042	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57009357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57575459	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58025924	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58621288	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58766761	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59802870	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61263937	0.82[EUR][1000 genomes]
rs61491513	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61729114	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260717	0.88[EUR][1000 genomes]
rs62260756	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262060	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262095	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262096	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262099	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262100	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262104	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262105	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262116	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262117	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262136	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62262138	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262144	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262145	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262148	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263578	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263580	0.88[EUR][1000 genomes]
rs62263584	0.88[EUR][1000 genomes]
rs62263586	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263588	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263590	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263591	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263600	0.87[AMR][1000 genomes]
rs6797500	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813644	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9859813	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49918800-49928400	Weak transcription	Colonic Mucosa	Colon
2	chr3:49919400-49928600	Weak transcription	Esophagus	oesophagus
3	chr3:49919600-49933400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:49919600-49933400	Weak transcription	Stomach Mucosa	stomach
5	chr3:49919600-49937800	Weak transcription	Small Intestine	intestine
6	chr3:49919800-49933800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:49920000-49930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:49920200-49932600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:49920200-49932600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:49920200-49938400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:49920400-49938200	Weak transcription	Left Ventricle	heart
13	chr3:49920600-49938200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:49920600-49938200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:49921800-49928600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:49922600-49935400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:49924000-49929400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:49924000-49929400	Strong transcription	Lung	lung
19	chr3:49924000-49930000	Strong transcription	Gastric	stomach
20	chr3:49924000-49930200	Strong transcription	NHEK	skin
21	chr3:49924000-49936000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:49924000-49937600	Strong transcription	Fetal Stomach	stomach
23	chr3:49924200-49929400	Strong transcription	Hela-S3	cervix
24	chr3:49924200-49930000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:49924200-49932600	Weak transcription	Pancreas	Pancrea
26	chr3:49924600-49937600	Weak transcription	K562	blood
27	chr3:49924800-49938200	Weak transcription	Right Ventricle	heart
28	chr3:49925000-49930400	Strong transcription	Fetal Intestine Small	intestine
29	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
30	chr3:49925600-49929600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:49926400-49929400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr3:49926600-49938400	Weak transcription	Aorta	Aorta
33	chr3:49926800-49927800	Weak transcription	HMEC	breast
34	chr3:49926800-49932600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:49927000-49932600	Weak transcription	Spleen	Spleen
36	chr3:49927000-49938000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:49927200-49928600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:49927200-49929000	Strong transcription	Fetal Intestine Large	intestine
39	chr3:49927200-49929800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:49927400-49929000	Strong transcription	Fetal Brain Female	brain
41	chr3:49927400-49936800	Weak transcription	Fetal Thymus	thymus
42	chr3:49927400-49937600	Weak transcription	Placenta	Placenta
43	chr3:49927600-49927800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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