Variant report

Variant	rs6465654
Chromosome Location	chr7:97786282-97786283
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	chr7:97785345..97788078-chr7:97789745..97792184,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11762534	1.00[ASW][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11763970	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11764933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11765552	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11767962	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768309	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670686	0.82[AMR][1000 genomes]
rs12674083	0.82[AMR][1000 genomes]
rs13221758	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17435590	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17435847	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34307903	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34320230	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801294	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465657	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465658	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6946915	0.87[AMR][1000 genomes]
rs6958572	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6965016	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967926	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6969384	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6977321	0.91[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7791463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804318	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808528	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7812180	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6465654	TSC22D4	cis	cerebellum	SCAN
rs6465654	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs6465654	BAIAP2L1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97762600-97793000	Weak transcription	Fetal Heart	heart
2	chr7:97763200-97792600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:97763400-97801000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:97763400-97821000	Weak transcription	NHLF	lung
5	chr7:97763600-97788400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr7:97763600-97793000	Weak transcription	NH-A	brain
7	chr7:97763600-97814200	Weak transcription	Osteobl	bone
8	chr7:97763600-97815800	Weak transcription	HSMM	muscle
9	chr7:97764000-97806200	Weak transcription	Psoas Muscle	Psoas
10	chr7:97765800-97840800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:97766000-97795000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:97766200-97790000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:97766600-97798400	Weak transcription	HSMMtube	muscle
14	chr7:97768800-97807000	Weak transcription	Stomach Mucosa	stomach
15	chr7:97771800-97797800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:97772400-97821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:97775600-97803600	Weak transcription	K562	blood
18	chr7:97777600-97789200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:97777800-97790600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:97778000-97790000	Strong transcription	Primary T cells from cord blood	blood
21	chr7:97778800-97792800	Weak transcription	Small Intestine	intestine
22	chr7:97779800-97789800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr7:97780000-97789400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:97780200-97792000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:97780400-97792000	Strong transcription	Fetal Intestine Large	intestine
26	chr7:97780600-97786800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:97780600-97787000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:97780600-97787200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:97780600-97787400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:97780600-97787400	Strong transcription	Fetal Muscle Leg	muscle
31	chr7:97780600-97787600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:97780600-97790000	Strong transcription	HepG2	liver
33	chr7:97780800-97786400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:97780800-97786600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr7:97780800-97786800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:97780800-97787400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr7:97780800-97787400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr7:97780800-97787400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr7:97780800-97787400	Strong transcription	Dnd41	blood
40	chr7:97780800-97787800	Strong transcription	Ovary	ovary
41	chr7:97780800-97788000	Strong transcription	Thymus	Thymus
42	chr7:97780800-97788200	Strong transcription	Fetal Thymus	thymus
43	chr7:97780800-97788400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:97780800-97789200	Strong transcription	Primary B cells from cord blood	blood
45	chr7:97780800-97789400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr7:97780800-97789400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:97780800-97789800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:97780800-97790000	Strong transcription	Liver	Liver
49	chr7:97781000-97786400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr7:97781000-97789200	Strong transcription	H1 Cell Line	embryonic stem cell

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