Variant report

Variant	rs7071211
Chromosome Location	chr10:98738428-98738429
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	ATF2	chr10:98738299-98738953	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:98738424-98738607	K562	blood:	n/a	n/a
3	NFIC	chr10:98738146-98738981	GM12878	blood:	n/a	n/a
4	CEBPB	chr10:98738173-98738886	GM12878	blood:	n/a	n/a
5	EBF1	chr10:98738362-98738791	GM12878	blood:	n/a	n/a
6	EP300	chr10:98738310-98738780	GM12878	blood:	n/a	chr10:98738576-98738590
7	ATF2	chr10:98738167-98738979	GM12878	blood:	n/a	n/a
8	NFATC1	chr10:98738256-98738913	GM12878	blood:	n/a	n/a
9	BHLHE40	chr10:98738414-98738857	GM12878	blood:	n/a	n/a
10	RUNX3	chr10:98738218-98739039	GM12878	blood:	n/a	n/a
11	EP300	chr10:98738238-98738784	GM12878	blood:	n/a	chr10:98738576-98738590
12	FOXM1	chr10:98738219-98738850	GM12878	blood:	n/a	n/a
13	BATF	chr10:98738342-98738707	GM12878	blood:	n/a	n/a
14	RUNX3	chr10:98738315-98738889	GM12878	blood:	n/a	n/a
15	NFIC	chr10:98738265-98738789	GM12878	blood:	n/a	n/a
16	BATF	chr10:98738302-98738877	GM12878	blood:	n/a	n/a
17	BCLAF1	chr10:98738206-98738854	GM12878	blood:	n/a	chr10:98738581-98738590
18	IRF4	chr10:98738177-98738818	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98736544..98739434-chr10:98740857..98743238,3	K562	blood:
2	chr10:98736543..98739434-chr10:98740164..98742956,2	K562	blood:

Variant related genes	Relation type
C10orf12	TF binding region
ENSG00000155640	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10437452	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188929	1.00[ASN][1000 genomes]
rs11188937	0.93[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11188939	0.93[ASW][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs11188940	0.82[EUR][1000 genomes]
rs11188947	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11188954	0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11188955	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11188956	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11188959	0.93[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs11188967	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11188971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11188978	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188999	1.00[ASN][1000 genomes]
rs12240946	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241405	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241564	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242330	0.86[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs12243551	0.93[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12244490	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246067	1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12247344	0.86[EUR][1000 genomes]
rs12248349	1.00[ASN][1000 genomes]
rs12249381	0.93[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12249427	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12249891	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12250548	1.00[ASN][1000 genomes]
rs12252424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12252435	0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs12254525	1.00[ASN][1000 genomes]
rs12256424	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12257413	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12258355	0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12258469	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12259265	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12261278	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12261881	0.82[EUR][1000 genomes]
rs12262784	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12263331	0.89[EUR][1000 genomes]
rs12264014	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264950	1.00[ASN][1000 genomes]
rs12265242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12265606	1.00[ASN][1000 genomes]
rs12266068	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12266185	0.82[EUR][1000 genomes]
rs12267926	1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12268216	1.00[ASW][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12268272	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13376965	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17112175	0.93[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs17112190	0.93[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs2104785	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2183449	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439735	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28505353	1.00[ASN][1000 genomes]
rs28758432	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4394767	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55855950	1.00[ASN][1000 genomes]
rs56327223	1.00[ASN][1000 genomes]
rs56867696	0.89[EUR][1000 genomes]
rs57501540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57716318	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs58270704	1.00[ASN][1000 genomes]
rs58376960	0.87[EUR][1000 genomes]
rs58409956	1.00[ASN][1000 genomes]
rs59751908	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59938221	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs59999388	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60576681	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61492214	0.89[EUR][1000 genomes]
rs6584101	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072273	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7073150	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081197	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082316	0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7082838	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085822	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7085851	0.89[EUR][1000 genomes]
rs7086875	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090441	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090690	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090880	1.00[ASN][1000 genomes]
rs72821721	1.00[ASN][1000 genomes]
rs72821744	1.00[ASN][1000 genomes]
rs72821759	1.00[ASN][1000 genomes]
rs73318637	1.00[ASN][1000 genomes]
rs73318641	1.00[ASN][1000 genomes]
rs73320607	1.00[ASN][1000 genomes]
rs74153734	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893325	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893564	0.81[AFR][1000 genomes]
rs7894138	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894418	0.82[EUR][1000 genomes]
rs7895914	1.00[ASN][1000 genomes]
rs7906294	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910221	0.93[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs7918085	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7920238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921193	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7921216	0.82[EUR][1000 genomes]
rs7921885	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831951	chr10:98717103-98761280	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7071211	CRTAC1	cis	parietal	SCAN
rs7071211	CCNJ	cis	cerebellum	SCAN
rs7071211	CWF19L1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98715400-98740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:98715400-98740600	Weak transcription	Aorta	Aorta
3	chr10:98715400-98740600	Weak transcription	Esophagus	oesophagus
4	chr10:98715600-98740600	Weak transcription	Fetal Stomach	stomach
5	chr10:98715600-98740600	Weak transcription	NHEK	skin
6	chr10:98715800-98740600	Weak transcription	Lung	lung
7	chr10:98716000-98740200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:98716000-98740400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:98716000-98740600	Weak transcription	Brain Anterior Caudate	brain
10	chr10:98716000-98740600	Weak transcription	Gastric	stomach
11	chr10:98716000-98740600	Weak transcription	Left Ventricle	heart
12	chr10:98716000-98740600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:98716000-98741000	Weak transcription	Brain Germinal Matrix	brain
14	chr10:98716200-98740800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:98716400-98740600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr10:98716600-98739800	Weak transcription	Primary T cells from cord blood	blood
17	chr10:98716600-98740600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr10:98716600-98740600	Weak transcription	Ovary	ovary
19	chr10:98716600-98740600	Weak transcription	HMEC	breast
20	chr10:98716600-98743200	Weak transcription	Hela-S3	cervix
21	chr10:98716800-98740600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:98717000-98740600	Weak transcription	Fetal Kidney	kidney
23	chr10:98717400-98740600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:98717800-98740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:98718600-98740400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr10:98718600-98740600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:98719000-98740600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:98719000-98740600	Weak transcription	Dnd41	blood
29	chr10:98719800-98740600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr10:98720000-98739200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr10:98720000-98740400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:98720000-98740600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:98720000-98740600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:98720400-98740600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr10:98720800-98741400	Weak transcription	NHLF	lung
36	chr10:98723000-98740600	Weak transcription	Fetal Lung	lung
37	chr10:98723400-98740400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:98723400-98740600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:98723400-98740600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr10:98723400-98740600	Weak transcription	Brain Substantia Nigra	brain
41	chr10:98724000-98740600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr10:98728200-98740400	Weak transcription	Osteobl	bone
43	chr10:98728400-98740600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:98728400-98740600	Weak transcription	HSMM	muscle
45	chr10:98728600-98741000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr10:98728800-98740600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:98731400-98740600	Weak transcription	Pancreas	Pancrea
48	chr10:98731400-98741200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr10:98731800-98745600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr10:98732000-98740800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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