Variant report

Variant	rs2228075
Chromosome Location	chr7:128034629-128034630
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127982337..127986134-chr7:128031866..128036135,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238750	Chromatin interaction
ENSG00000106344	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10954184	0.90[ASN][1000 genomes]
rs11765023	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs11765126	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs11773251	0.96[ASN][1000 genomes]
rs11973781	0.93[ASN][1000 genomes]
rs11977296	0.85[ASN][1000 genomes]
rs11981766	0.85[ASN][1000 genomes]
rs11982673	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs11983847	0.93[ASN][1000 genomes]
rs12536006	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706850	0.88[ASN][1000 genomes]
rs12706851	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13221784	0.89[CEU][hapmap];0.93[ASN][1000 genomes]
rs13222212	0.85[ASN][1000 genomes]
rs13227646	0.85[ASN][1000 genomes]
rs13242340	0.93[ASN][1000 genomes]
rs13312278	0.98[ASN][1000 genomes]
rs2076805	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs34848853	0.91[ASN][1000 genomes]
rs35649907	0.85[ASN][1000 genomes]
rs4566975	0.92[CHD][hapmap]
rs61283864	0.90[AFR][1000 genomes]
rs6975115	0.85[ASN][1000 genomes]
rs7802305	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv889191	chr7:127973133-128073326	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv608400	chr7:127978820-128048194	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	esv2493565	chr7:127985695-128053377	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3478325	chr7:127986726-128053483	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3478326	chr7:127986726-128053483	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2228075	ZC3HC1	cis	cerebellum	SCAN
rs2228075	ZNF800	cis	parietal	SCAN
rs2228075	IMPDH1	cis	cerebellum	SCAN
rs2228075	ATP6V1F	cis	parietal	SCAN
rs2228075	IMPDH1	cis	Adipose Subcutaneous	GTEx
rs2228075	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128002400-128044400	Weak transcription	Right Atrium	heart
2	chr7:128027800-128042800	Weak transcription	Fetal Brain Male	brain
3	chr7:128028000-128035600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:128028000-128045200	Weak transcription	Small Intestine	intestine
5	chr7:128028200-128036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr7:128028200-128036800	Weak transcription	Dnd41	blood
7	chr7:128028200-128037000	Weak transcription	Liver	Liver
8	chr7:128028400-128044600	Weak transcription	Fetal Heart	heart
9	chr7:128028800-128035600	Weak transcription	NHDF-Ad	bronchial
10	chr7:128028800-128037200	Weak transcription	Primary B cells from cord blood	blood
11	chr7:128029200-128037400	Weak transcription	Fetal Kidney	kidney
12	chr7:128029400-128037000	Weak transcription	HSMM	muscle
13	chr7:128029400-128037000	Weak transcription	NH-A	brain
14	chr7:128029600-128044400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:128029800-128037200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:128030000-128036000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:128030000-128036200	Weak transcription	HepG2	liver
18	chr7:128030000-128043800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:128030200-128037000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:128030200-128037200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:128030200-128040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:128030400-128036400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:128030400-128037200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:128030400-128037400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:128030400-128038400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:128031000-128043800	Strong transcription	Fetal Stomach	stomach
27	chr7:128031200-128037200	Weak transcription	Hela-S3	cervix
28	chr7:128031200-128038400	Strong transcription	Primary T cells from cord blood	blood
29	chr7:128031200-128039000	Strong transcription	Thymus	Thymus
30	chr7:128031200-128043200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:128031200-128043200	Strong transcription	A549	lung
32	chr7:128031200-128043600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:128031200-128043600	Strong transcription	Lung	lung
34	chr7:128031200-128044200	Strong transcription	Spleen	Spleen
35	chr7:128031400-128041800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr7:128031400-128043200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:128031400-128043200	Strong transcription	Gastric	stomach
38	chr7:128031400-128043600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:128031400-128044000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:128031400-128044200	Strong transcription	Fetal Muscle Leg	muscle
41	chr7:128031600-128035600	Strong transcription	Pancreas	Pancrea
42	chr7:128031600-128038400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr7:128031600-128038600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:128031600-128040800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:128031600-128041400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr7:128031600-128041600	Strong transcription	Brain Germinal Matrix	brain
47	chr7:128031600-128041800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:128031600-128042000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:128031600-128042000	Strong transcription	Right Ventricle	heart
50	chr7:128031600-128042200	Strong transcription	Fetal Brain Female	brain

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