Variant report

Variant	rs806172
Chromosome Location	chr7:127297002-127297003
allele	C/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	chr7:127296755-127297394	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127296504..127298380-chr7:127323608..127326210,2	K562	blood:

Variant related genes	Relation type
ENSG00000240790	TF binding region
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11772303	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12539411	0.82[AMR][1000 genomes]
rs12540484	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12667197	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12668077	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs12673293	0.80[AMR][1000 genomes]
rs1419967	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16871926	0.82[AMR][1000 genomes]
rs17151229	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17151377	0.85[AMR][1000 genomes]
rs17151470	0.83[AMR][1000 genomes]
rs2058457	0.82[AMR][1000 genomes]
rs2402871	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2582717	1.00[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap]
rs327510	0.85[CHB][hapmap]
rs327512	0.85[CHB][hapmap]
rs327516	0.85[CHB][hapmap]
rs3735644	1.00[LWK][hapmap]
rs3757778	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3757780	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808088	0.80[ASN][1000 genomes]
rs3824003	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4728079	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4731377	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56185520	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58106688	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59140894	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62481385	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62481416	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62481419	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62481443	0.80[ASN][1000 genomes]
rs67338333	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs698406	0.90[CHB][hapmap]
rs698408	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712697	0.90[CHB][hapmap]
rs712700	0.90[CHB][hapmap]
rs712701	0.90[CHB][hapmap]
rs712703	0.90[CHB][hapmap]
rs712704	0.90[CHB][hapmap];1.00[LWK][hapmap]
rs712707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712715	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712718	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs712719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs765971	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs806166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs806169	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806174	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs806175	0.95[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs806180	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs806188	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs806193	0.93[CHB][hapmap]
rs806214	1.00[LWK][hapmap]
rs882694	0.82[AMR][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	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs806172	GCC1	cis	lymphoblastoid	seeQTL
rs806172	GPR37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127293000-127304000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:127293200-127302200	Weak transcription	Aorta	Aorta
3	chr7:127293200-127304200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:127293200-127306000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:127293200-127306000	Weak transcription	Fetal Brain Female	brain
6	chr7:127293200-127322000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:127293200-127326600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:127293600-127297200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:127293800-127297400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr7:127294200-127299000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:127294400-127301600	Weak transcription	Fetal Brain Male	brain
12	chr7:127294600-127307400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:127294800-127297600	Weak transcription	Placenta	Placenta
14	chr7:127294800-127306200	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:127294800-127307400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:127294800-127327400	Weak transcription	Fetal Kidney	kidney
17	chr7:127295000-127297400	Genic enhancers	Dnd41	blood
18	chr7:127295000-127298600	Weak transcription	Gastric	stomach
19	chr7:127295000-127299600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:127295000-127299600	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:127295000-127300400	Weak transcription	Brain Substantia Nigra	brain
22	chr7:127295000-127300800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:127295000-127301200	Weak transcription	Fetal Lung	lung
24	chr7:127295000-127302000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:127295000-127302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:127295000-127303800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:127295000-127307400	Weak transcription	Esophagus	oesophagus
28	chr7:127295000-127314000	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:127295000-127314000	Weak transcription	Ovary	ovary
30	chr7:127295000-127314000	Weak transcription	Spleen	Spleen
31	chr7:127295000-127315600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr7:127295000-127318400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:127295000-127322200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:127295200-127297200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr7:127295200-127297600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:127295200-127298600	Weak transcription	Adipose Nuclei	Adipose
37	chr7:127295200-127299200	Weak transcription	HUVEC	blood vessel
38	chr7:127295200-127299400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr7:127295200-127300800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:127295200-127301000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:127295200-127305600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:127295200-127305800	Weak transcription	Colonic Mucosa	Colon
43	chr7:127295200-127306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:127295200-127317800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:127295200-127321800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:127295400-127299400	Weak transcription	HMEC	breast
47	chr7:127295400-127306800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:127295400-127326400	Weak transcription	Thymus	Thymus
49	chr7:127295600-127297200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr7:127295600-127300400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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