Variant report

Variant	rs10230965
Chromosome Location	chr7:128222966-128222967
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1013515	0.86[ASN][1000 genomes]
rs10231476	0.80[ASN][1000 genomes]
rs10232401	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10243297	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246093	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10246261	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10251475	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271590	0.82[ASN][1000 genomes]
rs10488627	0.95[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs11980741	1.00[JPT][hapmap]
rs12381410	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12386692	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672625	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs1560214	1.00[JPT][hapmap]
rs2288548	1.00[JPT][hapmap]
rs2288549	1.00[JPT][hapmap]
rs2562730	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2562733	1.00[JPT][hapmap]
rs2562737	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2562740	1.00[JPT][hapmap]
rs2732394	1.00[JPT][hapmap]
rs2732429	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs28479078	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28525628	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28526579	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28670000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28788212	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339075	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs339092	0.95[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs4642561	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4728108	1.00[JPT][hapmap]
rs4731448	1.00[JPT][hapmap]
rs4731453	1.00[JPT][hapmap]
rs4731454	1.00[JPT][hapmap]
rs5009156	0.82[ASN][1000 genomes]
rs58979384	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6467190	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6943009	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73463166	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73465114	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73465147	0.86[ASN][1000 genomes]
rs73465150	0.80[ASN][1000 genomes]
rs73465155	0.83[ASN][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	esv1848097	chr7:128179503-128248497	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv1810084	chr7:128201902-128248697	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1829966	chr7:128201902-128248697	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1847512	chr7:128201902-128248697	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv966885	chr7:128212815-128256300	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10230965	RP11-274B21.4	cis	Whole Blood	GTEx
rs10230965	FAM71F2	cis	cerebellum	SCAN
rs10230965	C7orf54	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
2	chr7:128173000-128231800	Weak transcription	Colonic Mucosa	Colon
3	chr7:128173000-128231800	Weak transcription	Fetal Kidney	kidney
4	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:128174000-128231800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:128174000-128232600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:128175400-128231800	Weak transcription	Left Ventricle	heart
8	chr7:128177600-128231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:128179200-128231800	Weak transcription	Esophagus	oesophagus
10	chr7:128181800-128231800	Weak transcription	Aorta	Aorta
11	chr7:128187600-128232000	Weak transcription	NH-A	brain
12	chr7:128188000-128232800	Weak transcription	Fetal Brain Female	brain
13	chr7:128188200-128229800	Weak transcription	HSMM	muscle
14	chr7:128188400-128230800	Weak transcription	Primary T cells from cord blood	blood
15	chr7:128188400-128231200	Weak transcription	Pancreas	Pancrea
16	chr7:128188800-128231800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:128191200-128226000	Weak transcription	Ovary	ovary
18	chr7:128191400-128232000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:128197800-128241800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:128199400-128231800	Weak transcription	HSMMtube	muscle
21	chr7:128200000-128258800	Weak transcription	Right Ventricle	heart
22	chr7:128201600-128225200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:128201600-128225600	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:128204800-128258800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:128205200-128231800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:128205400-128224600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr7:128208200-128233000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:128208800-128231800	Weak transcription	HMEC	breast
29	chr7:128208800-128232600	Weak transcription	Brain Substantia Nigra	brain
30	chr7:128211000-128231800	Weak transcription	Psoas Muscle	Psoas
31	chr7:128212800-128233000	Weak transcription	Brain Germinal Matrix	brain
32	chr7:128213200-128231800	Weak transcription	Brain Angular Gyrus	brain
33	chr7:128213400-128231800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:128213400-128238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:128214000-128231800	Weak transcription	Brain Anterior Caudate	brain
36	chr7:128214400-128231800	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:128214400-128231800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:128215200-128225600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:128215200-128231800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:128215200-128231800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:128215200-128232600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:128215200-128232800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:128215400-128231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:128215400-128231800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:128215400-128231800	Weak transcription	HUVEC	blood vessel
46	chr7:128215600-128224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:128215800-128223600	Weak transcription	Fetal Intestine Small	intestine
48	chr7:128215800-128224200	Weak transcription	Thymus	Thymus
49	chr7:128215800-128224600	Weak transcription	HepG2	liver
50	chr7:128215800-128225600	Weak transcription	Fetal Muscle Trunk	muscle

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