Variant report

Variant	rs7082838
Chromosome Location	chr10:98712188-98712189
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98711866..98714396-chr10:98719836..98721704,3	K562	blood:
2	chr10:98590745..98593944-chr10:98709452..98713107,4	MCF-7	breast:
3	chr10:98696795..98699148-chr10:98710595..98712314,2	K562	blood:

Variant related genes	Relation type
ENSG00000196233	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10437452	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188929	1.00[ASN][1000 genomes]
rs11188937	0.86[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes]
rs11188939	0.87[ASW][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs11188940	0.88[EUR][1000 genomes]
rs11188947	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11188954	0.88[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs11188955	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11188956	0.87[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];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11188959	0.87[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes]
rs11188967	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11188971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11188978	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188999	1.00[ASN][1000 genomes]
rs12240946	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241564	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242330	1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12243551	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[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];0.93[EUR][1000 genomes]
rs12244490	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246067	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12247344	0.91[EUR][1000 genomes]
rs12248349	1.00[ASN][1000 genomes]
rs12249381	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12249427	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12249891	0.88[EUR][1000 genomes]
rs12250548	1.00[ASN][1000 genomes]
rs12252424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12252435	0.83[YRI][hapmap];0.88[EUR][1000 genomes]
rs12254525	1.00[ASN][1000 genomes]
rs12256424	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12257413	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12258355	0.88[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs12258469	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12259265	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12261278	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12261881	0.88[EUR][1000 genomes]
rs12262784	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[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12263331	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12264014	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264950	1.00[ASN][1000 genomes]
rs12265242	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12265606	1.00[ASN][1000 genomes]
rs12266068	0.88[EUR][1000 genomes]
rs12266185	0.88[EUR][1000 genomes]
rs12267926	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12268216	0.93[ASW][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12268272	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13376965	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17112175	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17112190	0.87[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes]
rs2104785	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2183449	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439735	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28505353	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28758432	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4394767	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55855950	1.00[ASN][1000 genomes]
rs56327223	1.00[ASN][1000 genomes]
rs56867696	0.95[EUR][1000 genomes]
rs57501540	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57716318	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs58270704	1.00[ASN][1000 genomes]
rs58376960	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs58409956	1.00[ASN][1000 genomes]
rs59751908	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs59938221	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs59999388	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60576681	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61492214	0.95[EUR][1000 genomes]
rs6584101	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071211	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]
rs7072273	0.87[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];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7073150	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081197	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082316	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7085822	0.93[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7085851	0.95[EUR][1000 genomes]
rs7086875	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090441	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090690	0.82[AMR][1000 genomes];0.91[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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893325	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893564	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7894138	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894418	0.88[EUR][1000 genomes]
rs7895914	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906294	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910221	0.87[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes]
rs7918085	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];0.88[EUR][1000 genomes]
rs7920238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921193	0.88[EUR][1000 genomes]
rs7921216	0.88[EUR][1000 genomes]
rs7921885	0.93[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7082838	CRTAC1	cis	parietal	SCAN
rs7082838	CCNJ	cis	cerebellum	SCAN
rs7082838	CWF19L1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98611000-98713000	Weak transcription	Aorta	Aorta
2	chr10:98639800-98714600	Weak transcription	Esophagus	oesophagus
3	chr10:98640600-98714600	Weak transcription	Hela-S3	cervix
4	chr10:98653400-98714200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr10:98659000-98714600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:98663000-98720400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr10:98663600-98714800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:98664800-98714000	Weak transcription	Colonic Mucosa	Colon
9	chr10:98665000-98714800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:98666000-98714600	Weak transcription	Fetal Brain Female	brain
11	chr10:98669400-98714400	Weak transcription	HMEC	breast
12	chr10:98671200-98714600	Weak transcription	Ovary	ovary
13	chr10:98671200-98719800	Weak transcription	Fetal Brain Male	brain
14	chr10:98672400-98714600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:98675600-98714600	Weak transcription	Fetal Thymus	thymus
16	chr10:98675800-98714600	Weak transcription	Lung	lung
17	chr10:98675800-98714600	Weak transcription	Spleen	Spleen
18	chr10:98675800-98714800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr10:98679800-98724800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr10:98683200-98714800	Weak transcription	HSMMtube	muscle
21	chr10:98683800-98714600	Weak transcription	Osteobl	bone
22	chr10:98684000-98714600	Weak transcription	HepG2	liver
23	chr10:98684200-98713000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:98686000-98714600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:98686200-98714800	Weak transcription	Brain Angular Gyrus	brain
26	chr10:98689000-98714400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:98689200-98714800	Weak transcription	Brain Substantia Nigra	brain
28	chr10:98690600-98713200	Weak transcription	Gastric	stomach
29	chr10:98695400-98714600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:98695800-98714800	Weak transcription	Fetal Lung	lung
31	chr10:98697200-98713800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:98697200-98714600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr10:98697200-98714600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:98697200-98714600	Weak transcription	Fetal Muscle Leg	muscle
35	chr10:98697200-98714600	Weak transcription	NHLF	lung
36	chr10:98697200-98715000	Weak transcription	Brain Germinal Matrix	brain
37	chr10:98697600-98714800	Weak transcription	K562	blood
38	chr10:98698000-98713000	Weak transcription	Left Ventricle	heart
39	chr10:98698200-98713000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr10:98698200-98713000	Weak transcription	Fetal Stomach	stomach
41	chr10:98698200-98713000	Weak transcription	Thymus	Thymus
42	chr10:98698400-98714800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr10:98699000-98714800	Weak transcription	Fetal Kidney	kidney
44	chr10:98699600-98714800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr10:98700000-98712800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:98700000-98714600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:98702400-98713000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr10:98702800-98714600	Weak transcription	A549	lung
49	chr10:98703200-98714600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:98703400-98714600	Weak transcription	Brain Anterior Caudate	brain

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