Variant report

Variant	rs7774597
Chromosome Location	chr6:149820948-149820949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149818918..149821487-chr6:149828653..149831549,2	K562	blood:
2	chr6:149820594..149823333-chr6:149826797..149829564,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10485097	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782310	0.81[CHB][hapmap]
rs10782312	0.81[CHB][hapmap]
rs11155662	0.81[CHB][hapmap]
rs11155670	0.81[CHB][hapmap]
rs11155671	0.81[CHB][hapmap]
rs1125107	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12234128	0.81[CHB][hapmap]
rs12524946	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12529698	0.81[CHB][hapmap]
rs12663698	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665533	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474640	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17732745	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064520	0.81[CHB][hapmap]
rs2105200	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341550	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2341551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2341768	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28580659	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2880075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34870994	0.83[ASN][1000 genomes]
rs3734295	0.81[CHB][hapmap]
rs3777949	0.81[CHB][hapmap]
rs3798761	0.81[CHB][hapmap]
rs3813675	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924871	0.81[CHB][hapmap]
rs4869797	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897128	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4897130	0.87[ASN][1000 genomes]
rs4897131	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897132	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897133	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897137	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897138	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897139	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60404985	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62439778	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62442787	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442788	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62442789	0.95[ASN][1000 genomes]
rs62442790	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62442792	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62442793	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62442795	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62442798	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570968	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911016	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929614	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761617	0.80[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7740278	0.81[CHB][hapmap]
rs7753560	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767622	0.81[CHB][hapmap]
rs7774559	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9285521	0.81[CHB][hapmap]
rs9322184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322185	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322188	0.80[CHB][hapmap]
rs9322198	0.81[CHB][hapmap]
rs9322200	0.80[CHB][hapmap]
rs9322209	0.81[CHB][hapmap]
rs9373594	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9373595	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373596	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9377220	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377221	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377224	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9377230	0.81[CHB][hapmap]
rs9390684	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390687	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390688	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390689	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393175	0.80[CHB][hapmap]
rs9399689	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399690	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9404042	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9404043	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9404044	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9404048	0.81[CHB][hapmap]
rs9406344	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9498368	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9689569	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9689723	0.81[CHB][hapmap]
rs9718079	0.81[CHB][hapmap]
rs9767105	0.81[CHB][hapmap]
rs9767123	0.81[CHB][hapmap]
rs9767555	0.81[CHB][hapmap]
rs9767713	0.81[CHB][hapmap]
rs9800580	0.81[CHB][hapmap]
rs9800614	0.81[CHB][hapmap]
rs9800648	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9800686	0.81[CHB][hapmap]
rs9800736	0.81[CHB][hapmap]
rs9968911	0.81[CHB][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	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer 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
2	esv1832313	chr6:149789511-149840750	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7774597	GINM1	cis	Thyroid	GTEx
rs7774597	LRP11	cis	cerebellum	SCAN
rs7774597	LRP11	cis	parietal	SCAN
rs7774597	PPIL4	cis	cerebellum	SCAN
rs7774597	PPIL4	cis	parietal	SCAN
rs7774597	LATS1	cis	parietal	SCAN
rs7774597	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149804400-149824600	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:149806400-149832000	Weak transcription	HSMMtube	muscle
3	chr6:149806400-149844800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:149806800-149825200	Weak transcription	HSMM	muscle
5	chr6:149806800-149832400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:149807000-149832200	Weak transcription	Lung	lung
7	chr6:149807000-149849000	Weak transcription	Gastric	stomach
8	chr6:149807200-149824800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:149807200-149832000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:149807200-149835000	Weak transcription	Spleen	Spleen
11	chr6:149807200-149842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:149810400-149821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:149810800-149851600	Weak transcription	Esophagus	oesophagus
14	chr6:149811200-149860600	Weak transcription	Aorta	Aorta
15	chr6:149811400-149826600	Weak transcription	Fetal Intestine Small	intestine
16	chr6:149814800-149825200	Weak transcription	Fetal Thymus	thymus
17	chr6:149815200-149825600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:149815600-149824800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:149815600-149845000	Weak transcription	Small Intestine	intestine
20	chr6:149816600-149825200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:149817000-149830800	Weak transcription	Brain Angular Gyrus	brain
22	chr6:149817600-149821600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:149817600-149822200	Weak transcription	Primary B cells from cord blood	blood
24	chr6:149817800-149821600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:149817800-149829000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:149818000-149825400	Weak transcription	NHDF-Ad	bronchial
27	chr6:149818200-149821000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:149818200-149824600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr6:149818200-149830400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:149818400-149825600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:149818400-149826400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:149818400-149843800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:149818600-149822400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:149818600-149826600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:149818800-149821000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:149818800-149828200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:149818800-149845000	Weak transcription	A549	lung
38	chr6:149819000-149827200	Weak transcription	GM12878-XiMat	blood
39	chr6:149819200-149832000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:149819400-149821000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:149819400-149825400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:149819400-149825600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:149819400-149828800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:149819600-149821000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr6:149819600-149821400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr6:149819600-149821600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:149819600-149822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:149819800-149825400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:149819800-149828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:149820000-149822800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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