Variant report

Variant	rs6003579
Chromosome Location	chr22:23573867-23573868
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:23568645..23571293-chr22:23572654..23574460,2	MCF-7	breast:
2	chr22:23534743..23537175-chr22:23572328..23575055,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1005184	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1010609	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557496	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1557497	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2156921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213172	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267013	0.89[JPT][hapmap]
rs2267016	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs4820548	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4822375	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5751611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5759650	0.81[ASN][1000 genomes]
rs5759652	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5759655	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs743585	0.81[ASN][1000 genomes]
rs762601	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9608086	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915235	chr22:22971768-23650987	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
2	esv3388845	chr22:22973346-23652447	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	100 gene(s)	inside rSNPs	diseases
3	nsv531799	chr22:22993679-23642142	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
4	nsv1061433	chr22:22997799-23649107	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
5	nsv521695	chr22:22998337-23648009	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv915236	chr22:22998337-23650987	Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv588512	chr22:22998337-23667731	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv531800	chr22:23002708-23648163	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
9	nsv916593	chr22:23002709-23648790	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
10	nsv993496	chr22:23002709-23654222	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
11	nsv1067002	chr22:23007167-23643363	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv1067324	chr22:23007367-23654223	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv533839	chr22:23012013-23643223	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
14	nsv916933	chr22:23012069-23654237	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
15	nsv531801	chr22:23028586-23657804	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
16	nsv531802	chr22:23046186-23627391	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	diseases
17	nsv1060509	chr22:23055148-23648719	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
18	nsv1056324	chr22:23055148-23750989	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
19	nsv1062780	chr22:23060449-23648719	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
20	nsv948942	chr22:23063178-23645718	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
21	nsv1063200	chr22:23097177-23643224	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
22	nsv949250	chr22:23157485-23645718	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
23	nsv1057659	chr22:23400739-24138788	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
24	nsv588598	chr22:23530168-23638025	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv9876	chr22:23563331-23923059	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6003579	SLC7A4	cis	cerebellum	SCAN
rs6003579	BCR	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23566600-23578200	Weak transcription	Ovary	ovary
2	chr22:23566600-23579400	Weak transcription	Fetal Kidney	kidney
3	chr22:23566800-23575200	Weak transcription	HepG2	liver
4	chr22:23568000-23580200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr22:23569000-23586200	Weak transcription	A549	lung
6	chr22:23569600-23579800	Weak transcription	Small Intestine	intestine
7	chr22:23569800-23575400	Weak transcription	Pancreas	Pancrea
8	chr22:23570000-23575200	Weak transcription	NHLF	lung
9	chr22:23570000-23589800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr22:23570200-23574000	Weak transcription	Esophagus	oesophagus
11	chr22:23570200-23574800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr22:23570200-23577600	Weak transcription	NHEK	skin
13	chr22:23570200-23578000	Weak transcription	Stomach Mucosa	stomach
14	chr22:23570200-23578200	Weak transcription	Aorta	Aorta
15	chr22:23570200-23578400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr22:23571000-23576000	Weak transcription	HUVEC	blood vessel
17	chr22:23571000-23585400	Weak transcription	Hela-S3	cervix
18	chr22:23571400-23577200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:23571600-23574000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr22:23571600-23575800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr22:23571600-23576200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:23571600-23576800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr22:23571800-23574000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr22:23571800-23574000	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr22:23571800-23574800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:23571800-23574800	Strong transcription	Thymus	Thymus
27	chr22:23571800-23575600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr22:23571800-23575800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr22:23571800-23577000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr22:23571800-23577000	Enhancers	HSMMtube	muscle
31	chr22:23571800-23578200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr22:23571800-23578800	Weak transcription	Primary T cells from cord blood	blood
33	chr22:23571800-23580000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr22:23571800-23583600	Weak transcription	Dnd41	blood
35	chr22:23572000-23574200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr22:23572000-23574400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:23572000-23574800	Weak transcription	Brain Germinal Matrix	brain
38	chr22:23572000-23575000	Enhancers	Lung	lung
39	chr22:23572000-23575400	Weak transcription	Osteobl	bone
40	chr22:23572000-23575800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr22:23572000-23578600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr22:23572200-23574000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:23572200-23574200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr22:23572200-23575200	Weak transcription	Fetal Intestine Small	intestine
45	chr22:23572200-23576800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr22:23572200-23579400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr22:23572200-23583400	Weak transcription	HMEC	breast
48	chr22:23572400-23574000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr22:23572400-23581000	Enhancers	Brain Anterior Caudate	brain
50	chr22:23572600-23574000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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