Variant report

Variant	rs7610022
Chromosome Location	chr3:194999996-194999997
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194997826..195001793-chr3:195162641..195164811,3	MCF-7	breast:
2	chr3:194997928..195000350-chr3:195025041..195026973,2	K562	blood:
3	chr3:194998941..195000493-chr3:195162798..195164960,2	MCF-7	breast:
4	chr3:194990005..194994037-chr3:194997788..195001012,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XXYLT1-2	chr3:194999763-195000157	NONHSAT094149

Variant related genes	Relation type
ENSG00000114331	Chromatin interaction
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10933706	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11718218	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927933	0.80[ASN][1000 genomes]
rs13062574	0.93[ASN][1000 genomes]
rs1832667	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050809	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050810	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410803	0.88[EUR][1000 genomes]
rs2410839	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410840	0.93[ASN][1000 genomes]
rs28375276	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688106	0.86[ASN][1000 genomes]
rs2898570	0.86[EUR][1000 genomes]
rs3087885	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773418	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677671	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677820	0.93[ASN][1000 genomes]
rs4677825	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677830	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58204696	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437467	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780743	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781643	0.91[EUR][1000 genomes]
rs6791601	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6791943	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792029	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793035	0.80[EUR][1000 genomes]
rs6795263	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73080837	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73080839	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612694	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638924	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7640100	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643947	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7644002	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649142	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823297	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823298	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823299	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823303	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823304	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823305	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823307	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823308	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823309	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823312	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823313	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823533	0.80[ASN][1000 genomes]
rs823534	0.80[ASN][1000 genomes]
rs862066	0.80[ASN][1000 genomes]
rs9288747	0.86[ASN][1000 genomes]
rs9831944	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832920	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860389	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863901	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878312	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992400-195009000	Weak transcription	Spleen	Spleen
2	chr3:194992600-195003600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:194992600-195003600	Weak transcription	Small Intestine	intestine
4	chr3:194992600-195008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:194992600-195008800	Weak transcription	Lung	lung
6	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
7	chr3:194992800-195003600	Weak transcription	Esophagus	oesophagus
8	chr3:194992800-195003600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:194992800-195003600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:194992800-195003600	Weak transcription	Left Ventricle	heart
11	chr3:194992800-195003600	Weak transcription	Psoas Muscle	Psoas
12	chr3:194992800-195003600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:194992800-195004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:194992800-195005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:194992800-195008600	Weak transcription	Ovary	ovary
16	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
17	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
18	chr3:194993000-195001200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:194993000-195003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:194993000-195003400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:194993000-195003400	Weak transcription	Adipose Nuclei	Adipose
22	chr3:194993000-195003600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:194993000-195003600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:194993000-195003600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:194993000-195003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:194993000-195003600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:194993000-195003600	Weak transcription	Fetal Stomach	stomach
28	chr3:194993000-195003600	Weak transcription	Gastric	stomach
29	chr3:194993000-195003600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:194993000-195003600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:194993000-195003600	Weak transcription	Stomach Mucosa	stomach
32	chr3:194993000-195003800	Weak transcription	Fetal Brain Female	brain
33	chr3:194993000-195003800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:194993000-195004000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:194993000-195004800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:194993000-195005000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:194993000-195005200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:194993000-195005600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:194993000-195005600	Weak transcription	HSMM	muscle
40	chr3:194993000-195005600	Weak transcription	HSMMtube	muscle
41	chr3:194993000-195006200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:194993000-195006200	Weak transcription	Brain Anterior Caudate	brain
43	chr3:194993000-195006800	Weak transcription	NHLF	lung
44	chr3:194993000-195007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:194993000-195007000	Weak transcription	Brain Substantia Nigra	brain
46	chr3:194993000-195007200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:194993000-195007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:194993000-195008200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:194993000-195008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:194993000-195008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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