Variant report

Variant	rs6946968
Chromosome Location	chr7:102758084-102758085
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	chr7:102758076-102758206	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102733221..102734992-chr7:102757778..102759973,2	MCF-7	breast:
2	chr7:102705659..102708585-chr7:102755906..102758111,2	K562	blood:
3	chr7:102714071..102718258-chr7:102757961..102760938,3	K562	blood:
4	chr7:102743045..102745303-chr7:102756742..102758546,2	K562	blood:

Variant related genes	Relation type
NAPEPLD	TF binding region
ENSG00000170632	Chromatin interaction
ENSG00000161040	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10229137	1.00[EUR][1000 genomes]
rs10230292	1.00[EUR][1000 genomes]
rs10240086	1.00[EUR][1000 genomes]
rs10260344	0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10264869	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10268112	1.00[EUR][1000 genomes]
rs10268849	0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808122	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10808123	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808124	1.00[EUR][1000 genomes]
rs10808125	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808126	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10808127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10953379	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs11560367	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11760826	1.00[EUR][1000 genomes]
rs11765948	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11772979	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11773883	1.00[EUR][1000 genomes]
rs11981558	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12155099	1.00[EUR][1000 genomes]
rs12539639	1.00[EUR][1000 genomes]
rs13225565	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13226097	1.00[EUR][1000 genomes]
rs13242079	0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13247932	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1404213	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs1477159	1.00[EUR][1000 genomes]
rs1477161	1.00[EUR][1000 genomes]
rs1477162	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1477163	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1558853	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1861725	1.00[EUR][1000 genomes]
rs1861726	1.00[EUR][1000 genomes]
rs1861728	0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1861730	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1861732	1.00[EUR][1000 genomes]
rs1968198	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1968199	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1968202	1.00[EUR][1000 genomes]
rs1974715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1974716	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2015289	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2041949	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2098447	1.00[EUR][1000 genomes]
rs2111381	1.00[EUR][1000 genomes]
rs2193418	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2411078	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2411079	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2411081	1.00[EUR][1000 genomes]
rs2411082	0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2898640	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181009	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4294127	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4295594	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4374923	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4440560	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4530973	0.82[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4727560	1.00[EUR][1000 genomes]
rs4727561	0.86[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729868	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729869	1.00[EUR][1000 genomes]
rs4729870	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729871	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729872	1.00[EUR][1000 genomes]
rs4729874	0.83[AMR][1000 genomes]
rs4729875	1.00[EUR][1000 genomes]
rs4729876	1.00[EUR][1000 genomes]
rs4729878	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729882	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729883	1.00[EUR][1000 genomes]
rs4729884	0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729892	1.00[EUR][1000 genomes]
rs56938507	1.00[EUR][1000 genomes]
rs59179196	1.00[EUR][1000 genomes]
rs59182081	1.00[EUR][1000 genomes]
rs60006777	1.00[EUR][1000 genomes]
rs61187383	1.00[EUR][1000 genomes]
rs61676871	1.00[EUR][1000 genomes]
rs62622397	1.00[EUR][1000 genomes]
rs6465890	0.85[YRI][hapmap]
rs6465891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6465892	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6465893	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6465898	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6465902	1.00[EUR][1000 genomes]
rs6465904	0.87[AMR][1000 genomes]
rs6465905	1.00[EUR][1000 genomes]
rs6465907	1.00[EUR][1000 genomes]
rs6465911	1.00[EUR][1000 genomes]
rs6944809	1.00[EUR][1000 genomes]
rs6945578	1.00[EUR][1000 genomes]
rs6946989	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947777	1.00[EUR][1000 genomes]
rs6950177	0.80[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6955436	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6959711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6964822	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6966872	0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6966961	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6973702	1.00[EUR][1000 genomes]
rs6973787	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6976034	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6976290	1.00[EUR][1000 genomes]
rs6976794	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6977206	0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979140	1.00[EUR][1000 genomes]
rs6979470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73408223	1.00[EUR][1000 genomes]
rs73408251	1.00[EUR][1000 genomes]
rs73408254	1.00[EUR][1000 genomes]
rs73408255	1.00[EUR][1000 genomes]
rs73408259	1.00[EUR][1000 genomes]
rs73408285	1.00[EUR][1000 genomes]
rs73408286	1.00[EUR][1000 genomes]
rs73410119	1.00[EUR][1000 genomes]
rs73410129	1.00[EUR][1000 genomes]
rs73410143	1.00[EUR][1000 genomes]
rs73412168	1.00[EUR][1000 genomes]
rs73412171	1.00[EUR][1000 genomes]
rs73412175	1.00[EUR][1000 genomes]
rs7349957	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7350051	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7782147	1.00[EUR][1000 genomes]
rs7783856	0.80[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7784337	0.80[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792240	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7801969	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs7807900	1.00[EUR][1000 genomes]
rs7811224	1.00[EUR][1000 genomes]
rs9640672	1.00[EUR][1000 genomes]
rs9641307	1.00[EUR][1000 genomes]
rs9641308	1.00[EUR][1000 genomes]
rs9649256	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9649257	0.82[AFR][1000 genomes]
rs9691829	1.00[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	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6946968	SVH	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102716600-102760200	Weak transcription	Lung	lung
2	chr7:102716600-102762200	Weak transcription	Colonic Mucosa	Colon
3	chr7:102716600-102768200	Weak transcription	Right Ventricle	heart
4	chr7:102716800-102768400	Weak transcription	Stomach Mucosa	stomach
5	chr7:102717600-102770200	Weak transcription	Small Intestine	intestine
6	chr7:102717800-102768000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:102719400-102769600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:102724000-102760000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:102724000-102770200	Weak transcription	Psoas Muscle	Psoas
10	chr7:102725200-102770200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:102725600-102760200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:102725800-102770000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr7:102727800-102768000	Weak transcription	Fetal Brain Male	brain
14	chr7:102728000-102760000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:102730200-102760200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:102730200-102769600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:102734200-102770600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:102736000-102768000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:102738400-102767800	Weak transcription	Pancreas	Pancrea
20	chr7:102738400-102768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:102738400-102773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:102738600-102761200	Weak transcription	Placenta	Placenta
23	chr7:102741400-102770600	Weak transcription	HUVEC	blood vessel
24	chr7:102741800-102759200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:102743000-102761800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:102743600-102770200	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:102744400-102759200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr7:102744400-102760200	Weak transcription	GM12878-XiMat	blood
29	chr7:102745000-102760000	Weak transcription	Aorta	Aorta
30	chr7:102745600-102760200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr7:102746000-102759200	Weak transcription	HSMM	muscle
32	chr7:102747200-102759400	Weak transcription	Gastric	stomach
33	chr7:102747200-102762600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:102747200-102768200	Weak transcription	Fetal Heart	heart
35	chr7:102747400-102758800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:102747400-102759000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr7:102747400-102766400	Weak transcription	Brain Germinal Matrix	brain
38	chr7:102747400-102781800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:102747600-102759000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr7:102747600-102759800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr7:102747600-102760000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr7:102747600-102760200	Weak transcription	Thymus	Thymus
43	chr7:102747600-102761800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:102747600-102768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:102747600-102768000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:102747600-102775200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:102747600-102789200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:102747800-102760000	Weak transcription	HepG2	liver
49	chr7:102753200-102758400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:102753200-102764800	Strong transcription	Fetal Intestine Large	intestine

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