Variant report

Variant	rs9296979
Chromosome Location	chr6:15530784-15530785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15529195..15531595-chr6:15533933..15536941,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JARID2-2	chr6:15530735-15531421	NONHSAT107874

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1018381	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1018382	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1040410	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949305	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11752196	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11752598	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11753919	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11755055	0.93[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11757499	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11759609	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13437303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16876554	0.82[CEU][hapmap]
rs16876555	0.82[CEU][hapmap]
rs16876671	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1997679	0.83[ASN][1000 genomes]
rs2076058	0.82[CEU][hapmap]
rs2205852	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237110	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs2619516	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619519	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619521	1.00[JPT][hapmap]
rs2619522	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2619526	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619528	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2619529	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619530	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2619533	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2619534	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2619535	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619540	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619541	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619544	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619545	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2619546	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619548	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619552	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743548	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743549	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743550	0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743551	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2743552	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2743553	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2743853	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743854	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743857	1.00[JPT][hapmap]
rs2743858	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743859	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743860	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743861	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743864	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743865	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743866	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743867	0.93[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743869	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743870	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743871	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2743872	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3778651	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs6459408	0.83[ASN][1000 genomes]
rs6903159	0.83[ASN][1000 genomes]
rs734129	0.93[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs760761	1.00[JPT][hapmap]
rs7752070	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7770921	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs875463	0.86[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9296975	1.00[CEU][hapmap]
rs9296976	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296977	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296978	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296980	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296981	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296984	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9296985	0.93[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296987	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296988	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9464793	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9464794	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9464795	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9464797	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9464801	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9464802	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9464803	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9464805	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9464807	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476835	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9476836	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9476837	0.93[ASW][hapmap];0.82[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9476838	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9476839	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9476840	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9476841	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9476842	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9476844	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9476845	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9476846	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9476849	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9476854	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476858	0.93[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476859	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476860	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476863	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476865	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476866	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476867	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476868	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476869	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9476883	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9654600	0.82[CEU][hapmap]

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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv428473	chr6:15522653-15595739	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15507000-15533200	Weak transcription	HSMM	muscle
2	chr6:15512600-15531000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:15512600-15536400	Weak transcription	Psoas Muscle	Psoas
4	chr6:15515800-15533600	Strong transcription	Thymus	Thymus
5	chr6:15518400-15531400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:15519400-15534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:15523000-15533800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:15523400-15534000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:15523400-15534400	Weak transcription	HUVEC	blood vessel
10	chr6:15523600-15535800	Weak transcription	Small Intestine	intestine
11	chr6:15523600-15540000	Weak transcription	NHEK	skin
12	chr6:15523800-15533400	Weak transcription	HMEC	breast
13	chr6:15523800-15534200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:15524200-15535800	Weak transcription	Stomach Mucosa	stomach
15	chr6:15524400-15533800	Weak transcription	NHDF-Ad	bronchial
16	chr6:15524400-15535400	Weak transcription	A549	lung
17	chr6:15524400-15549400	Weak transcription	Hela-S3	cervix
18	chr6:15524600-15531400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:15524600-15536600	Weak transcription	Right Ventricle	heart
20	chr6:15524800-15530800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:15524800-15530800	Weak transcription	Esophagus	oesophagus
22	chr6:15524800-15531400	Weak transcription	Left Ventricle	heart
23	chr6:15524800-15532400	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:15524800-15533800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:15524800-15534200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:15524800-15536600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:15524800-15549800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:15525000-15531000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:15525000-15531200	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:15525000-15531400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:15525000-15532800	Weak transcription	Fetal Brain Female	brain
32	chr6:15525000-15534000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:15525000-15534000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:15525000-15536000	Weak transcription	NHLF	lung
35	chr6:15525000-15536400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:15525000-15536600	Weak transcription	Colonic Mucosa	Colon
37	chr6:15525000-15539000	Weak transcription	Brain Angular Gyrus	brain
38	chr6:15525000-15553400	Weak transcription	Ovary	ovary
39	chr6:15525200-15532200	Weak transcription	Brain Germinal Matrix	brain
40	chr6:15525200-15533400	Weak transcription	Placenta	Placenta
41	chr6:15525200-15536400	Weak transcription	Adipose Nuclei	Adipose
42	chr6:15525400-15531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:15525400-15539000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:15525600-15530800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:15525800-15533400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:15526600-15531000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:15526800-15531000	Weak transcription	HepG2	liver
48	chr6:15526800-15531200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:15526800-15532200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:15527000-15531200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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