Variant report

Variant	rs3769161
Chromosome Location	chr2:174066475-174066476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:174060729..174063071-chr2:174065159..174066981,2	K562	blood:
2	chr2:174064115..174068320-chr2:174070790..174075190,5	K562	blood:
3	chr2:174065896..174068842-chr2:174070151..174072535,2	MCF-7	breast:
4	chr2:174059743..174062229-chr2:174064774..174066981,2	K562	blood:
5	chr2:174066171..174068320-chr2:174072504..174075190,2	K562	blood:
6	chr2:174065533..174067512-chr2:174076722..174079013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238133	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10930579	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615166	0.84[ASN][1000 genomes]
rs12986917	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs12987496	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12989116	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12990553	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12997078	0.84[ASN][1000 genomes]
rs12998711	0.84[ASN][1000 genomes]
rs13008554	0.85[ASN][1000 genomes]
rs13017210	0.83[ASN][1000 genomes]
rs13017438	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13022800	0.81[CHB][hapmap]
rs13029949	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs13032010	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17302977	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs17761169	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076857	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289397	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289399	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34658268	0.88[ASN][1000 genomes]
rs34702663	0.80[ASN][1000 genomes]
rs36103648	0.86[ASN][1000 genomes]
rs3754741	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3754743	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3754744	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3769157	0.94[ASN][1000 genomes]
rs3769167	0.89[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769187	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3769192	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769194	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4972533	0.88[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs55913048	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56151459	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56342397	0.80[ASN][1000 genomes]
rs6433395	0.81[CHB][hapmap]
rs71417423	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
3	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
5	chr2:174049000-174070600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:174049200-174070200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
8	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
9	chr2:174049600-174074400	Weak transcription	Fetal Stomach	stomach
10	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:174053400-174072000	Weak transcription	Right Atrium	heart
12	chr2:174053400-174075600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:174053400-174078400	Weak transcription	Gastric	stomach
14	chr2:174053400-174082000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:174053400-174089800	Weak transcription	Pancreas	Pancrea
16	chr2:174057400-174075800	Weak transcription	Hela-S3	cervix
17	chr2:174058000-174112800	Weak transcription	Spleen	Spleen
18	chr2:174059000-174075000	Weak transcription	NHLF	lung
19	chr2:174060000-174075200	Weak transcription	Fetal Kidney	kidney
20	chr2:174060200-174092600	Weak transcription	Aorta	Aorta
21	chr2:174060600-174066600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:174061000-174082000	Weak transcription	Fetal Brain Female	brain
23	chr2:174061200-174097600	Weak transcription	Lung	lung
24	chr2:174061400-174092200	Weak transcription	Brain Substantia Nigra	brain
25	chr2:174061600-174070200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:174061600-174074600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:174061600-174077000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:174061600-174083200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:174061600-174083200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:174061800-174072600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:174061800-174075200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:174061800-174080200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:174062000-174071600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:174062600-174069400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:174063200-174074400	Weak transcription	Psoas Muscle	Psoas
36	chr2:174063600-174067400	Weak transcription	Ovary	ovary
37	chr2:174063600-174074400	Weak transcription	Left Ventricle	heart
38	chr2:174063600-174075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:174063600-174097600	Weak transcription	HSMM	muscle
40	chr2:174063800-174066600	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:174063800-174066600	Weak transcription	A549	lung
42	chr2:174063800-174067800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:174063800-174068600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:174063800-174069000	Weak transcription	Fetal Heart	heart
45	chr2:174063800-174069000	Weak transcription	NHEK	skin
46	chr2:174063800-174069800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:174063800-174070000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:174063800-174070200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:174063800-174070200	Weak transcription	Placenta	Placenta
50	chr2:174063800-174075000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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