Variant report

Variant	rs885653
Chromosome Location	chr7:149414424-149414425
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	chr7:149414302-149414443	K562	blood:	n/a	n/a
2	WRNIP1	chr7:149414237-149414578	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:149410803..149414471-chr7:149419495..149421257,3	K562	blood:
2	chr7:149413328..149416314-chr7:149417568..149419723,2	MCF-7	breast:
3	chr7:149320371..149323534-chr7:149411288..149414666,4	K562	blood:

Variant related genes	Relation type
KRBA1	TF binding region
ENSG00000133619	Chromatin interaction
ENSG00000133624	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10231875	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10240931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[EUR][1000 genomes]
rs10256826	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs10256935	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10258658	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10262457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10952835	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11979707	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171280	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28647767	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55727837	0.92[EUR][1000 genomes]
rs56226490	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56265968	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60047316	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60647533	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66588543	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67491931	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67647638	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67657627	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68129719	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68139633	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966081	0.86[JPT][hapmap]
rs73479712	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7791608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs7804205	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7808442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs867152	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs885652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021849	chr7:149230929-149422239	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1034350	chr7:149264094-149666356	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv539190	chr7:149264094-149666356	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1023901	chr7:149364044-149747442	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv539191	chr7:149364044-149747442	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking 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 target site	40 gene(s)	inside rSNPs	diseases
6	nsv469576	chr7:149379626-149563233	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription 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 target site	21 gene(s)	inside rSNPs	diseases
7	nsv1031581	chr7:149386249-149570178	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv539192	chr7:149386249-149570178	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv465199	chr7:149398065-149462621	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv608979	chr7:149398065-149462621	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs885653	ZNF862	cis	cerebellum	SCAN
rs885653	ABCF2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149412600-149414600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:149412600-149414600	Flanking Active TSS	HMEC	breast
3	chr7:149412800-149415000	Enhancers	Psoas Muscle	Psoas
4	chr7:149412800-149416800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:149412800-149417000	Weak transcription	Liver	Liver
6	chr7:149412800-149417400	Weak transcription	Fetal Intestine Large	intestine
7	chr7:149412800-149418000	Weak transcription	Aorta	Aorta
8	chr7:149412800-149418600	Weak transcription	Primary B cells from cord blood	blood
9	chr7:149412800-149421400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:149412800-149438800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:149413000-149414800	Enhancers	Fetal Brain Male	brain
12	chr7:149413000-149415000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:149413000-149415000	Enhancers	Esophagus	oesophagus
14	chr7:149413000-149415600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:149413000-149416000	Weak transcription	Primary T cells from cord blood	blood
16	chr7:149413000-149416000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:149413000-149416000	Weak transcription	Fetal Intestine Small	intestine
18	chr7:149413000-149416000	Weak transcription	A549	lung
19	chr7:149413000-149416000	Weak transcription	NHLF	lung
20	chr7:149413000-149416200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:149413000-149416600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:149413000-149417200	Weak transcription	HSMMtube	muscle
23	chr7:149413000-149417400	Weak transcription	Thymus	Thymus
24	chr7:149413000-149418000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:149413000-149418000	Weak transcription	Small Intestine	intestine
26	chr7:149413000-149418200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:149413000-149418200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:149413000-149424000	Weak transcription	Fetal Kidney	kidney
29	chr7:149413000-149433200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:149413200-149414800	Enhancers	Colon Smooth Muscle	Colon
31	chr7:149413200-149416000	Weak transcription	Brain Substantia Nigra	brain
32	chr7:149413200-149416000	Weak transcription	Ovary	ovary
33	chr7:149413200-149416000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr7:149413200-149416400	Weak transcription	Osteobl	bone
35	chr7:149413200-149417800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:149413200-149417800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:149413200-149418000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:149413200-149418000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:149413200-149418400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:149413200-149421800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:149413200-149426200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr7:149413200-149432000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:149413200-149433600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr7:149413400-149414800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:149413400-149414800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:149413400-149414800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr7:149413400-149415000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:149413400-149415400	Enhancers	Left Ventricle	heart
49	chr7:149413400-149416000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:149413400-149416000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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