Variant report

Variant	rs17164371
Chromosome Location	chr7:128375372-128375373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:128374951-128379140	K562	blood:	n/a	n/a
2	RCOR1	chr7:128375087-128375387	K562	blood:	n/a	n/a
3	MAX	chr7:128374811-128375469	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:128354778..128357384-chr7:128375264..128377980,2	MCF-7	breast:
2	chr7:128335112..128337902-chr7:128374655..128377601,2	K562	blood:
3	chr7:128372524..128376128-chr7:128376580..128381119,6	MCF-7	breast:

Variant related genes	Relation type
CALU	TF binding region
ENSG00000128595	Chromatin interaction
ENSG00000252866	Chromatin interaction
ENSG00000201041	Chromatin interaction
ENSG00000135248	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2060717	1.00[ASW][hapmap]
rs2402933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2402934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339057	0.81[CHB][hapmap]
rs339059	0.80[CHB][hapmap]
rs339061	0.81[CHB][hapmap]
rs4731512	1.00[ASW][hapmap]
rs7780294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17164371	CCDC136	cis	cerebellum	SCAN
rs17164371	TMEM209	cis	parietal	SCAN
rs17164371	ZC3HC1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128349400-128378600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:128349800-128378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:128349800-128378400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:128361600-128378600	Weak transcription	Right Atrium	heart
5	chr7:128369200-128377800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:128369400-128377800	Weak transcription	HMEC	breast
7	chr7:128370400-128378200	Weak transcription	Spleen	Spleen
8	chr7:128370600-128377600	Weak transcription	HSMMtube	muscle
9	chr7:128371000-128378200	Enhancers	K562	blood
10	chr7:128373200-128377400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:128373200-128378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:128374000-128377800	Weak transcription	HUVEC	blood vessel
13	chr7:128374000-128378000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:128374400-128377000	Enhancers	Primary B cells from peripheral blood	blood
15	chr7:128374600-128376200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr7:128374600-128376600	Enhancers	Primary B cells from cord blood	blood
17	chr7:128374800-128375800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr7:128374800-128375800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr7:128374800-128376000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr7:128374800-128376200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:128375000-128375400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:128375000-128376200	Enhancers	Primary hematopoietic stem cells	blood
23	chr7:128375000-128376200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:128375200-128375400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:128375200-128375600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:128375200-128376400	Enhancers	Fetal Muscle Leg	muscle

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