Variant report

Variant	rs4949917
Chromosome Location	chr1:86076585-86076586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86046521..86048351-chr1:86075953..86079253,3	MCF-7	breast:
2	chr1:86041793..86044827-chr1:86073934..86077302,3	K562	blood:
3	chr1:86064019..86065868-chr1:86075742..86078671,2	K562	blood:
4	chr1:86073205..86075088-chr1:86076581..86078830,2	K562	blood:
5	chr1:86045659..86048173-chr1:86076180..86078969,3	MCF-7	breast:
6	chr1:86042110..86043822-chr1:86074708..86077302,2	K562	blood:

Variant related genes	Relation type
ENSG00000230285	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10747323	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747324	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs10873711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873718	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs10873719	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs1094353	0.86[AMR][1000 genomes]
rs1094360	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12037294	0.81[EUR][1000 genomes]
rs12405017	0.87[CHD][hapmap]
rs12757797	0.92[YRI][hapmap]
rs12758966	1.00[CEU][hapmap]
rs1360239	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481200	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1764287	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1764295	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1775985	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1775986	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1775987	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1775991	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1775992	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs1775993	0.87[CHD][hapmap]
rs2014733	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2014750	1.00[CEU][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs2026772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026773	0.86[ASW][hapmap];0.81[YRI][hapmap]
rs2026774	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2389973	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2389974	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs2389975	0.80[EUR][1000 genomes]
rs2970548	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap]
rs313724	0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs313725	0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs369999	1.00[CEU][hapmap]
rs381453	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs399547	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs401657	0.82[YRI][hapmap]
rs420515	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs425357	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs429040	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs430956	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[YRI][hapmap]
rs432254	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs4379699	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs438401	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs444875	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs450953	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs4949913	0.83[YRI][hapmap]
rs4949918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673975	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs6682235	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs6686719	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs6694808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521240	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7528385	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7529942	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs7533395	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535884	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs7547023	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs821378	1.00[ASW][hapmap];0.87[CHD][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap]
rs821380	0.96[YRI][hapmap]
rs821383	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs821385	0.81[AFR][1000 genomes]
rs821387	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs821388	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs821390	1.00[ASW][hapmap];0.87[CHD][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap]
rs821392	0.88[EUR][1000 genomes]
rs821397	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs821400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs821402	0.93[ASW][hapmap]
rs821403	0.96[YRI][hapmap]
rs849158	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9324152	1.00[ASW][hapmap];0.87[CHD][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap]
rs9324153	0.93[ASW][hapmap]
rs9651138	0.82[AMR][1000 genomes]
rs9661608	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9661951	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9701898	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9793556	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4949917	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:86070000-86076800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:86070600-86076600	Weak transcription	Fetal Stomach	stomach
5	chr1:86071200-86076600	Weak transcription	Fetal Lung	lung
6	chr1:86071200-86076800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:86071600-86076600	Enhancers	NHDF-Ad	bronchial
8	chr1:86071600-86078800	Enhancers	NHLF	lung
9	chr1:86071800-86076800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:86072200-86077600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:86072400-86076600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:86072400-86076600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:86073000-86078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:86073200-86076800	Weak transcription	Fetal Heart	heart
15	chr1:86073200-86077000	Weak transcription	Ovary	ovary
16	chr1:86073200-86078400	Weak transcription	Pancreas	Pancrea
17	chr1:86073200-86082200	Weak transcription	Aorta	Aorta
18	chr1:86073600-86076600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:86073600-86076800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:86073600-86078000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:86073800-86076600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:86073800-86077400	Weak transcription	HepG2	liver
23	chr1:86073800-86078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:86073800-86078600	Weak transcription	Hela-S3	cervix
25	chr1:86074000-86078400	Enhancers	A549	lung
26	chr1:86074200-86076600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:86074200-86077400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:86074200-86077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:86074200-86078000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:86074200-86078400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:86074200-86078400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:86074200-86078400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:86074200-86081200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:86074400-86076600	Weak transcription	Placenta	Placenta
35	chr1:86074400-86076800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:86074400-86076800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:86074400-86076800	Weak transcription	HMEC	breast
38	chr1:86074400-86077400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:86074400-86077400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:86074400-86077800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:86074400-86077800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:86074400-86078400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:86074600-86076600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:86074600-86077200	Weak transcription	Fetal Intestine Small	intestine
45	chr1:86074600-86077400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:86074600-86077600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:86074600-86077600	Weak transcription	HUVEC	blood vessel
48	chr1:86074800-86076800	Weak transcription	Fetal Intestine Large	intestine
49	chr1:86075200-86076600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:86075200-86076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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