Variant report

Variant	rs3748936
Chromosome Location	chr2:101009238-101009239
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	chr2:101005691..101009453-chr2:101017314..101020656,3	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10167159	0.86[AMR][1000 genomes]
rs10172841	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs10176978	0.83[ASN][1000 genomes]
rs10180570	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10180685	1.00[ASN][1000 genomes]
rs10183063	0.95[ASN][1000 genomes]
rs10184899	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10193535	1.00[ASW][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs10206374	1.00[ASW][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1057056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057063	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1057064	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1124009	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13391930	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13396147	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13400841	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13404823	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13407408	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13407648	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13407891	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13410582	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13419808	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1347721	0.90[AMR][1000 genomes]
rs1370627	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1437972	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.93[ASN][1000 genomes]
rs1465829	0.85[CHD][hapmap]
rs17024034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17024035	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17024129	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17024133	0.83[ASW][hapmap];0.90[GIH][hapmap]
rs17024136	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17024144	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17024203	1.00[CEU][hapmap];0.85[CHD][hapmap]
rs17024207	0.85[CHD][hapmap]
rs17024209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1898571	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1898573	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2083148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2309801	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3748934	0.85[CHD][hapmap]
rs3791358	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs4149506	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4149509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4149515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4149516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4149522	0.85[CHD][hapmap]
rs4850932	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4851276	1.00[CEU][hapmap]
rs55640826	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55843950	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55932868	0.93[ASN][1000 genomes]
rs56118658	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56656536	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs56741959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57862179	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58164864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58674788	0.93[ASN][1000 genomes]
rs58876304	0.88[AFR][1000 genomes]
rs59701896	0.93[ASN][1000 genomes]
rs59858985	0.93[ASN][1000 genomes]
rs60131548	0.88[AFR][1000 genomes]
rs60468180	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60566188	0.93[ASN][1000 genomes]
rs60609848	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60898093	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61321970	0.83[AMR][1000 genomes]
rs61710328	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542933	0.93[ASN][1000 genomes]
rs6542945	0.93[ASN][1000 genomes]
rs6542946	1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs6706707	0.93[ASN][1000 genomes]
rs6713862	0.88[AFR][1000 genomes]
rs6716009	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6716367	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6724695	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6725672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728575	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs6732285	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs6736938	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6738566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6739589	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6749572	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750040	1.00[CHB][hapmap]
rs6754869	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6757774	0.88[AFR][1000 genomes]
rs6758161	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6758622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761084	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72960184	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72960186	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72960202	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73966105	0.93[ASN][1000 genomes]
rs73966106	0.93[ASN][1000 genomes]
rs73968413	0.93[ASN][1000 genomes]
rs7559084	0.93[ASN][1000 genomes]
rs7559939	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7559946	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7561065	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562184	0.93[ASN][1000 genomes]
rs7562461	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7562479	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7562486	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7562615	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7562636	0.93[ASN][1000 genomes]
rs7562754	0.93[ASN][1000 genomes]
rs7564178	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7565502	0.93[ASN][1000 genomes]
rs7567130	0.95[ASN][1000 genomes]
rs7571410	0.93[ASN][1000 genomes]
rs7571651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7571659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs7572119	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7574684	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7575422	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7576749	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7580252	1.00[CEU][hapmap]
rs7582096	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7582546	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7585713	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7585898	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7587333	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs7596483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598205	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs7598227	0.93[ASN][1000 genomes]
rs7605834	0.93[ASN][1000 genomes]
rs876439	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs9308834	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]

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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv874701	chr2:100976139-101023261	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100993200-101017800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:100998200-101022600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:100998400-101010000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:101000400-101009400	Weak transcription	HepG2	liver
5	chr2:101002000-101023400	Weak transcription	Psoas Muscle	Psoas
6	chr2:101002400-101012000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:101003200-101021000	Weak transcription	K562	blood
8	chr2:101005200-101015000	Strong transcription	Fetal Brain Female	brain
9	chr2:101005600-101017600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:101005600-101032800	Weak transcription	HUVEC	blood vessel
11	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:101006000-101021600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:101006400-101018400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:101006600-101023600	Strong transcription	Brain Germinal Matrix	brain
15	chr2:101006600-101031600	Strong transcription	Fetal Stomach	stomach
16	chr2:101006800-101014800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:101007000-101025000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:101007000-101027200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr2:101007200-101011200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:101007200-101015400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:101007200-101018600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:101007200-101032000	Weak transcription	NHDF-Ad	bronchial
23	chr2:101007400-101009600	Weak transcription	Fetal Kidney	kidney
24	chr2:101007400-101010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:101007400-101011800	Weak transcription	Fetal Intestine Large	intestine
26	chr2:101007400-101014600	Strong transcription	Brain Cingulate Gyrus	brain
27	chr2:101007400-101014800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:101007400-101021600	Weak transcription	HSMMtube	muscle
29	chr2:101007600-101010400	Strong transcription	Left Ventricle	heart
30	chr2:101007600-101012800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr2:101007600-101013600	Strong transcription	Adipose Nuclei	Adipose
32	chr2:101007600-101013800	Strong transcription	Thymus	Thymus
33	chr2:101007600-101014800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:101007600-101014800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:101007600-101014800	Strong transcription	Fetal Intestine Small	intestine
36	chr2:101007600-101015000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:101007600-101015400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:101007600-101023400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:101007600-101024200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:101007600-101030600	Weak transcription	NH-A	brain
41	chr2:101007800-101009400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:101007800-101014400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:101007800-101014800	Strong transcription	Brain Anterior Caudate	brain
44	chr2:101007800-101014800	Strong transcription	Ovary	ovary
45	chr2:101007800-101015000	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:101007800-101021200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:101007800-101023800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:101007800-101024000	Weak transcription	Liver	Liver
49	chr2:101008000-101009600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:101008000-101011000	Strong transcription	Fetal Lung	lung

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