Variant report

Variant	rs3862937
Chromosome Location	chr1:169436678-169436679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169434628..169437236-chr1:169437830..169439900,2	K562	blood:
2	chr1:169435747..169436728-chr1:169515625..169516171,2	MCF-7	breast:
3	chr1:169428402..169430662-chr1:169436223..169440016,3	MCF-7	breast:
4	chr1:169436332..169438093-chr1:169441418..169443400,2	K562	blood:
5	chr1:169435618..169443312-chr1:169452571..169456844,11	MCF-7	breast:
6	chr1:169434650..169437970-chr1:169438181..169441761,3	MCF-7	breast:
7	chr1:169434019..169436756-chr1:169452207..169454585,3	MCF-7	breast:
8	chr1:169435452..169436972-chr1:169437830..169439463,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000234437	Chromatin interaction
ENSG00000117477	Chromatin interaction
ENSG00000234604	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10753786	0.83[CHB][hapmap]
rs10800447	0.82[CHB][hapmap]
rs10919173	0.89[CHB][hapmap]
rs12040141	1.00[CEU][hapmap]
rs12121994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12143193	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12145146	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12145226	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12727318	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12729761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12733001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12733037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12733626	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12744859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12752953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13306334	1.00[CEU][hapmap]
rs1517745	0.88[CHB][hapmap]
rs1533518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1533519	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16862081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16862097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16862133	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16862153	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862217	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16862236	0.85[EUR][1000 genomes]
rs1883167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2066001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2203743	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2271762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2272801	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2300158	0.83[CHB][hapmap]
rs2420015	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2420016	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3213586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3213587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs34057682	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34373126	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34599582	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34640648	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34858340	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34989506	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35171152	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35686518	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35918529	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3765229	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3766084	1.00[CEU][hapmap]
rs3766090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766097	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4140538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4140539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4551642	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4590731	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57295069	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58809384	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66512221	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6672589	0.89[CHB][hapmap]
rs66937324	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67795749	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72637232	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7528751	1.00[CEU][hapmap]
rs7551623	1.00[CEU][hapmap]
rs929133	0.94[CHB][hapmap]
rs9332623	1.00[CEU][hapmap]
rs9332624	1.00[CEU][hapmap]
rs9332628	1.00[CEU][hapmap]
rs9332647	1.00[CEU][hapmap]
rs9332658	1.00[CEU][hapmap]
rs9332678	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169429600-169448200	Weak transcription	Fetal Heart	heart
2	chr1:169429800-169436800	Weak transcription	Right Ventricle	heart
3	chr1:169429800-169446400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:169430000-169443800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:169430000-169444800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:169430000-169445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:169430000-169445600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:169430000-169446200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:169430000-169446200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:169430000-169446200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:169430000-169446400	Weak transcription	HUVEC	blood vessel
12	chr1:169430000-169450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:169430000-169452800	Weak transcription	HMEC	breast
19	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
20	chr1:169430000-169452800	Weak transcription	NHEK	skin
21	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
22	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
26	chr1:169430200-169436800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:169430200-169436800	Weak transcription	Fetal Brain Female	brain
28	chr1:169430200-169436800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:169430200-169442600	Weak transcription	Gastric	stomach
30	chr1:169430200-169444800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:169430200-169445400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:169430200-169445600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:169430200-169445600	Weak transcription	Fetal Stomach	stomach
34	chr1:169430200-169446200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:169430200-169446200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:169430200-169446200	Weak transcription	Lung	lung
37	chr1:169430200-169446200	Weak transcription	Pancreas	Pancrea
38	chr1:169430200-169446400	Weak transcription	Thymus	Thymus
39	chr1:169430200-169450600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:169430200-169451800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:169430200-169452600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:169430200-169452600	Weak transcription	NH-A	brain
43	chr1:169430200-169453200	Weak transcription	Esophagus	oesophagus
44	chr1:169430600-169446200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:169430600-169446200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:169430600-169452800	Weak transcription	Small Intestine	intestine
47	chr1:169430800-169446200	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:169431200-169446800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:169431200-169452000	Weak transcription	GM12878-XiMat	blood
50	chr1:169431400-169446200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links