Variant report

Variant	rs10401212
Chromosome Location	chr19:37402468-37402469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37402448..37404618-chr19:37405463..37407897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198453	Chromatin interaction
ENSG00000185869	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10404981	0.91[JPT][hapmap]
rs10407557	1.00[EUR][1000 genomes]
rs10408951	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10409206	0.87[EUR][1000 genomes]
rs10410594	0.91[JPT][hapmap]
rs10414781	0.86[EUR][1000 genomes]
rs10414907	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10416732	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10416960	0.93[JPT][hapmap]
rs10418144	1.00[EUR][1000 genomes]
rs10418176	0.84[JPT][hapmap]
rs10426008	0.91[EUR][1000 genomes]
rs11084868	0.89[EUR][1000 genomes]
rs12981965	1.00[JPT][hapmap]
rs13345230	0.81[EUR][1000 genomes]
rs1624293	0.91[JPT][hapmap]
rs16971771	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16971772	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16971850	1.00[JPT][hapmap]
rs17707101	0.93[JPT][hapmap]
rs2010342	0.85[EUR][1000 genomes]
rs2385470	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28626335	1.00[EUR][1000 genomes]
rs3816391	0.93[JPT][hapmap]
rs3955478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4006391	0.86[EUR][1000 genomes]
rs4006392	0.86[EUR][1000 genomes]
rs4805189	0.87[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap]
rs4805190	0.90[GIH][hapmap];0.92[JPT][hapmap];0.80[LWK][hapmap];0.81[MKK][hapmap]
rs4806376	0.82[EUR][1000 genomes]
rs486466	0.87[CHB][hapmap]
rs493482	0.87[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap]
rs497144	0.87[ASN][1000 genomes]
rs506463	0.84[GIH][hapmap]
rs553981	0.84[GIH][hapmap]
rs56387564	1.00[EUR][1000 genomes]
rs566432	0.87[CHB][hapmap]
rs60293110	1.00[EUR][1000 genomes]
rs62115573	0.86[EUR][1000 genomes]
rs62115574	0.97[EUR][1000 genomes]
rs62115611	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62115612	0.84[EUR][1000 genomes]
rs7257045	0.99[EUR][1000 genomes]
rs7257251	0.97[EUR][1000 genomes]
rs7257484	0.85[EUR][1000 genomes]
rs73626774	1.00[EUR][1000 genomes]
rs8101922	1.00[EUR][1000 genomes]
rs8112709	0.83[ASN][1000 genomes]
rs826263	0.81[JPT][hapmap]
rs9304878	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
13	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv458569	chr19:37331614-37412887	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv579462	chr19:37331614-37412887	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS 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
18	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
19	nsv524754	chr19:37383894-37403224	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37344400-37406400	ZNF genes & repeats	Liver	Liver
2	chr19:37346400-37404600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37353400-37405000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:37373800-37403400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:37374000-37405400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37374200-37404200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:37374400-37406400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37380400-37405000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:37391600-37403200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr19:37393000-37406200	Weak transcription	HUVEC	blood vessel
11	chr19:37393400-37406000	Weak transcription	NHLF	lung
12	chr19:37394400-37404200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr19:37395200-37403000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:37395200-37406800	Weak transcription	Stomach Mucosa	stomach
15	chr19:37395400-37406000	Weak transcription	NHEK	skin
16	chr19:37397200-37404600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:37397600-37406000	Weak transcription	Fetal Heart	heart
18	chr19:37398200-37405000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr19:37399200-37406000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:37399200-37406000	Weak transcription	NH-A	brain
21	chr19:37399400-37402600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:37399400-37402800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:37399400-37402800	Weak transcription	HSMM	muscle
24	chr19:37399400-37402800	Weak transcription	HSMMtube	muscle
25	chr19:37399400-37403800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:37399400-37406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:37399400-37406000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:37399400-37406000	Weak transcription	Esophagus	oesophagus
29	chr19:37399400-37406000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:37399400-37406200	Weak transcription	Colonic Mucosa	Colon
31	chr19:37399400-37406200	Weak transcription	Fetal Thymus	thymus
32	chr19:37399400-37406200	Weak transcription	Gastric	stomach
33	chr19:37399400-37406200	Weak transcription	Psoas Muscle	Psoas
34	chr19:37399600-37402600	Weak transcription	Thymus	Thymus
35	chr19:37399600-37405800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:37399600-37406000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:37399600-37406000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:37399600-37406000	Weak transcription	Fetal Brain Male	brain
39	chr19:37399600-37406000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:37399600-37406200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:37399600-37406200	Weak transcription	Brain Angular Gyrus	brain
42	chr19:37400000-37402600	Weak transcription	Placenta	Placenta
43	chr19:37400200-37406200	Weak transcription	Osteobl	bone
44	chr19:37400400-37402600	Weak transcription	Primary T cells from cord blood	blood
45	chr19:37400400-37402600	Weak transcription	Brain Substantia Nigra	brain
46	chr19:37400400-37406000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:37400400-37406000	Weak transcription	Fetal Kidney	kidney
48	chr19:37400400-37406200	Weak transcription	Colon Smooth Muscle	Colon
49	chr19:37400400-37406200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr19:37400400-37406200	Weak transcription	Fetal Muscle Leg	muscle

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