Variant report

Variant	rs6669168
Chromosome Location	chr1:171460027-171460028
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:171459635-171460136	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171458362..171461090-chr1:171478088..171481055,2	K562	blood:
2	chr1:171454578..171456452-chr1:171458968..171461203,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL425P	TF binding region
ENSG00000117523	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10913017	0.83[AFR][1000 genomes]
rs10913119	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10913149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913197	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs10913285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913292	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12076841	0.83[AFR][1000 genomes]
rs12080096	1.00[YRI][hapmap]
rs12562424	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12564279	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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038040	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2038041	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2038043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179882	1.00[ASW][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2294291	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs3204333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57562814	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60014783	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676140	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681173	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6702038	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72717832	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717839	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72717840	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72717853	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72717854	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7517178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521480	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7522026	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171455600-171461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:171455800-171461600	Weak transcription	Gastric	stomach
3	chr1:171455800-171465400	Weak transcription	Lung	lung
4	chr1:171455800-171467800	Weak transcription	Spleen	Spleen
5	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
6	chr1:171456200-171461600	Weak transcription	Left Ventricle	heart
7	chr1:171456200-171467800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:171456400-171460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:171456400-171460200	Enhancers	Liver	Liver
11	chr1:171456400-171460600	Enhancers	Colon Smooth Muscle	Colon
12	chr1:171456400-171461600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:171456400-171462400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:171456400-171462400	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:171456400-171466000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:171456400-171467200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:171456400-171467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:171456400-171468400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:171456400-171470200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:171456400-171471200	Weak transcription	Thymus	Thymus
21	chr1:171456400-171473000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
24	chr1:171456600-171460200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:171456600-171460200	Weak transcription	NHDF-Ad	bronchial
26	chr1:171456600-171460400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:171456600-171461600	Weak transcription	Psoas Muscle	Psoas
28	chr1:171456600-171467000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:171456600-171469600	Weak transcription	Fetal Stomach	stomach
30	chr1:171456800-171464200	Weak transcription	Fetal Brain Male	brain
31	chr1:171456800-171474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:171457000-171464000	Weak transcription	Fetal Kidney	kidney
33	chr1:171457000-171465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:171457200-171462000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:171457200-171469000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:171457600-171462400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:171457600-171463600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:171457600-171471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:171457800-171460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:171457800-171460400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:171457800-171461400	Weak transcription	Right Atrium	heart
42	chr1:171457800-171461600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:171457800-171462000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:171457800-171462000	Strong transcription	Fetal Thymus	thymus
45	chr1:171457800-171463400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:171457800-171463600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:171457800-171463800	Weak transcription	Aorta	Aorta
48	chr1:171457800-171463800	Weak transcription	Esophagus	oesophagus
49	chr1:171457800-171464600	Enhancers	Primary T cells from cord blood	blood
50	chr1:171457800-171482000	Weak transcription	Rectal Mucosa Donor 31	rectum

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