Variant report

Variant	rs7673610
Chromosome Location	chr4:76460536-76460537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10518140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11721925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722278	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11727806	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11729106	1.00[CEU][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11732511	1.00[CEU][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12648028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648354	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1351094	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]
rs1493705	0.83[JPT][hapmap]
rs17271259	0.83[JPT][hapmap]
rs17271540	0.82[JPT][hapmap]
rs1904104	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2126854	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306177	0.97[EUR][1000 genomes]
rs2903701	0.92[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3905796	0.83[JPT][hapmap]
rs6836107	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6845472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845588	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7683530	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7673610	THAP6	cis	Lymphoblastoid	GTEx
rs7673610	RCHY1	cis	parietal	SCAN
rs7673610	RCHY1	cis	cerebellum	SCAN
rs7673610	RCHY1	cis	lymphoblastoid	seeQTL
rs7673610	RCHY1	Cis_1M	lymphoblastoid	RTeQTL
rs7673610	THAP6	cis	multi-tissue	Pritchard
rs7673610	THAP6	cis	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76440400-76466400	Weak transcription	Small Intestine	intestine
2	chr4:76440400-76473200	Weak transcription	Gastric	stomach
3	chr4:76443400-76470200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:76444400-76461000	Weak transcription	A549	lung
5	chr4:76444400-76471800	Weak transcription	Fetal Brain Male	brain
6	chr4:76451600-76474400	Weak transcription	Psoas Muscle	Psoas
7	chr4:76452600-76468000	Weak transcription	NHLF	lung
8	chr4:76452600-76477400	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:76453200-76473600	Weak transcription	Brain Angular Gyrus	brain
10	chr4:76455000-76469400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:76455000-76470200	Weak transcription	Brain Substantia Nigra	brain
12	chr4:76455000-76470800	Weak transcription	NHDF-Ad	bronchial
13	chr4:76456000-76473000	Weak transcription	HepG2	liver
14	chr4:76456400-76471600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:76456600-76461600	Weak transcription	NH-A	brain
16	chr4:76456600-76467400	Weak transcription	HMEC	breast
17	chr4:76456600-76467400	Weak transcription	Osteobl	bone
18	chr4:76456600-76471000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:76456600-76473200	Weak transcription	Fetal Heart	heart
20	chr4:76456800-76464200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:76456800-76467600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:76456800-76467800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:76456800-76470000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:76456800-76472400	Weak transcription	Brain Anterior Caudate	brain
25	chr4:76456800-76474400	Weak transcription	HSMMtube	muscle
26	chr4:76457000-76468400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:76457000-76470200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:76457000-76470800	Weak transcription	HSMM	muscle
29	chr4:76457000-76471800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:76457000-76474400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:76458000-76464600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:76458000-76470200	Weak transcription	Right Ventricle	heart
33	chr4:76458200-76464400	Weak transcription	Ovary	ovary
34	chr4:76458200-76465000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:76458200-76467400	Weak transcription	Primary B cells from cord blood	blood
36	chr4:76458200-76468000	Weak transcription	Left Ventricle	heart
37	chr4:76458200-76470000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:76458200-76470200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:76458200-76470200	Weak transcription	Aorta	Aorta
40	chr4:76458200-76470200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr4:76458200-76472000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:76458200-76472000	Weak transcription	Thymus	Thymus
43	chr4:76458200-76472600	Weak transcription	Pancreas	Pancrea
44	chr4:76458200-76474400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:76458400-76464800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:76458400-76465800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:76458400-76467800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:76458400-76470000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:76458400-76470000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:76458400-76480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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