Variant report

Variant	rs3010190
Chromosome Location	chr1:227804310-227804311
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	chr1:227803218..227804951-chr1:227810975..227813465,2	MCF-7	breast:
2	chr1:227797816..227799614-chr1:227803015..227804639,2	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10047205	0.86[JPT][hapmap]
rs1021553	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1021554	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10495276	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10799423	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10799431	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799432	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799433	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799434	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916158	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916159	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916165	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916169	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916175	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916176	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916178	0.87[JPT][hapmap]
rs10916179	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916183	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916184	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916185	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11484723	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11580570	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12023298	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12025815	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12040302	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12070002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079123	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080590	0.91[JPT][hapmap]
rs12082414	0.91[JPT][hapmap]
rs12096675	0.82[JPT][hapmap]
rs12132444	1.00[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12740317	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1407718	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1495842	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1495845	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1495847	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1495849	0.81[JPT][hapmap]
rs16847966	0.91[JPT][hapmap]
rs16847991	0.91[JPT][hapmap]
rs16847992	0.91[JPT][hapmap]
rs16848029	0.82[JPT][hapmap]
rs1845758	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2018401	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088210	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088211	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088212	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088214	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2093609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2093610	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2132366	0.91[JPT][hapmap]
rs2132367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2201571	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453682	0.87[JPT][hapmap]
rs2644140	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644161	0.86[JPT][hapmap]
rs2814085	0.81[JPT][hapmap]
rs28407112	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2935145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2935146	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2935147	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2935152	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]
rs2935155	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2999741	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999743	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999744	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999745	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999746	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010186	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010191	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]
rs3010192	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010193	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010195	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3748806	0.86[JPT][hapmap]
rs4359006	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4376731	0.86[JPT][hapmap]
rs4653512	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653514	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653515	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653848	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653849	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653850	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653853	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6664682	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671825	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6683151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6697867	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7512348	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7523915	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7528094	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7539151	0.86[JPT][hapmap]
rs7539914	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7542685	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7551459	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903683	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903684	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903690	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs903694	0.82[JPT][hapmap]
rs903695	0.81[JPT][hapmap]
rs903697	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs951083	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs965942	0.91[JPT][hapmap]
rs976959	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945673	chr1:227799341-227819395	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:227794400-227804400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:227794600-227808600	Weak transcription	Left Ventricle	heart
6	chr1:227795200-227807000	Weak transcription	Fetal Heart	heart
7	chr1:227796200-227807200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:227796800-227806000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:227797600-227804800	ZNF genes & repeats	Fetal Stomach	stomach
10	chr1:227797800-227804800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:227797800-227805800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr1:227797800-227806400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr1:227797800-227807200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr1:227798000-227806400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr1:227798200-227806800	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr1:227798200-227806800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr1:227798200-227806800	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr1:227798200-227808000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:227799400-227805000	ZNF genes & repeats	Lung	lung
20	chr1:227800200-227805000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:227800200-227805600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:227800200-227820600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:227800400-227804600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:227800400-227805000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:227800400-227807000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:227800400-227814200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:227800600-227804800	Weak transcription	Gastric	stomach
28	chr1:227800800-227805000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:227801000-227807200	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr1:227801200-227821800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:227801400-227804400	Weak transcription	Brain Angular Gyrus	brain
32	chr1:227801600-227805200	ZNF genes & repeats	Liver	Liver
33	chr1:227801600-227805200	Weak transcription	Fetal Intestine Large	intestine
34	chr1:227802200-227806200	ZNF genes & repeats	Dnd41	blood
35	chr1:227802600-227806200	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr1:227802600-227808200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
37	chr1:227803000-227805800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
38	chr1:227803000-227806000	ZNF genes & repeats	Aorta	Aorta
39	chr1:227803200-227805400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:227803200-227806000	ZNF genes & repeats	A549	lung
41	chr1:227803400-227804600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:227803400-227806000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
43	chr1:227803400-227806200	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr1:227803600-227804600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:227803600-227805400	Strong transcription	Ovary	ovary
46	chr1:227803800-227804600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:227803800-227804600	Weak transcription	Pancreas	Pancrea
48	chr1:227803800-227805000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:227803800-227805600	Weak transcription	Colonic Mucosa	Colon
50	chr1:227803800-227806000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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