Variant report

Variant	rs1002127
Chromosome Location	chr11:73103835-73103836
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:73102033-73111863	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:73103217-73103921	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:73103820-73103868	K562	blood:	n/a	n/a
4	POLR2A	chr11:73102688-73107221	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr11:73103795-73104269	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:73098106-73111810	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:73103358-73104141	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:73103572-73103951	K562	blood:	n/a	n/a
9	POLR2A	chr11:73103384-73103839	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:73103458-73105097	GM12878	blood:	n/a	n/a
11	NR2F2	chr11:73103654-73103946	K562	blood:	n/a	n/a
12	POLR2A	chr11:73103307-73110889	A549	lung:	n/a	n/a
13	POLR2A	chr11:73103724-73103904	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:73103694-73104182	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr11:73103365-73103994	K562	blood:	n/a	n/a
16	POLR2A	chr11:73103462-73108498	GM12891	blood:	n/a	n/a
17	POLR2A	chr11:73103211-73111119	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:73102758-73107984	HL-60	blood:	n/a	n/a
19	POLR2A	chr11:73103338-73104454	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:73103575-73103906	GM12892	blood:	n/a	n/a
21	POLR2A	chr11:73103187-73103978	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:73102692-73103850	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr11:73103383-73111849	GM12892	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73086883..73089044-chr11:73102784..73104513,3	MCF-7	breast:
2	chr11:73065745..73068475-chr11:73103301..73106275,2	MCF-7	breast:

No data

Variant related genes	Relation type
RELT	TF binding region
ENSG00000054967	Chromatin interaction
ENSG00000266866	Chromatin interaction
ENSG00000110237	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10501411	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs11235770	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11235809	1.00[CEU][hapmap]
rs11544310	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544311	0.81[EUR][1000 genomes]
rs11821094	0.89[CEU][hapmap]
rs11823913	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11828904	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12099129	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12276892	1.00[CEU][hapmap]
rs12285885	1.00[CEU][hapmap]
rs12288753	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12290623	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17244596	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17244602	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17244616	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17310361	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17310374	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17851510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1938777	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2027760	0.89[CEU][hapmap]
rs2027761	0.89[CEU][hapmap]
rs2027763	0.89[CEU][hapmap]
rs2298469	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs28400367	1.00[ASN][1000 genomes]
rs34304845	0.80[AFR][1000 genomes]
rs3741149	0.89[CEU][hapmap]
rs3741152	0.89[CEU][hapmap]
rs60078907	0.86[EUR][1000 genomes]
rs60924672	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61345051	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105681	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7110369	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7112924	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114009	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7114376	1.00[CEU][hapmap]
rs7115055	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7115806	0.89[CEU][hapmap]
rs7118982	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7122825	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7123985	1.00[CEU][hapmap]
rs7125598	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7125949	0.89[CEU][hapmap]
rs7125978	0.89[CEU][hapmap]
rs7129990	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs724111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73542929	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542938	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542952	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542960	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542967	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542976	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542979	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542990	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930454	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7930880	0.89[CEU][hapmap]
rs7934218	1.00[CEU][hapmap]
rs7935948	1.00[CEU][hapmap]
rs7938391	1.00[CEU][hapmap]
rs7941359	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7944346	1.00[CEU][hapmap]
rs7945825	1.00[CEU][hapmap]
rs7951072	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7951174	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv897911	chr11:73044351-73108276	Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers 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 target site	48 gene(s)	inside rSNPs	diseases
4	esv3375921	chr11:73101854-73104652	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1002127	FAM168A	cis	Whole Blood	GTEx
rs1002127	ARHGEF17	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73091000-73104200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:73095200-73116200	Weak transcription	Liver	Liver
3	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:73096600-73104400	Weak transcription	Fetal Brain Male	brain
5	chr11:73097000-73106000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:73097200-73117600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:73097400-73106400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:73097400-73113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:73097600-73104600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:73097600-73106800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:73097600-73110200	Weak transcription	NHDF-Ad	bronchial
12	chr11:73097800-73104000	Weak transcription	Brain Germinal Matrix	brain
13	chr11:73098000-73104200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:73098600-73104600	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr11:73098600-73126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:73098600-73132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:73098800-73104800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:73098800-73105200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:73098800-73113000	Weak transcription	Fetal Brain Female	brain
20	chr11:73099000-73104800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:73099200-73106600	Strong transcription	Fetal Intestine Small	intestine
22	chr11:73099200-73112400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:73099400-73104800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:73099400-73109600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:73099400-73112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:73099400-73113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:73099600-73104200	Weak transcription	K562	blood
30	chr11:73099600-73105400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr11:73099600-73119200	Weak transcription	Fetal Lung	lung
32	chr11:73099800-73104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:73100000-73104800	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr11:73100000-73116600	Weak transcription	Pancreas	Pancrea
35	chr11:73100000-73118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:73100200-73104000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:73100200-73104400	Weak transcription	Fetal Heart	heart
38	chr11:73100200-73106400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:73100200-73117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:73100400-73104800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:73100400-73104800	Weak transcription	Colonic Mucosa	Colon
42	chr11:73100400-73109600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:73100400-73109800	Weak transcription	Right Atrium	heart
44	chr11:73100600-73104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr11:73100600-73104400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:73100600-73104600	Genic enhancers	NHEK	skin
47	chr11:73100600-73118600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:73100800-73104200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:73100800-73109800	Weak transcription	HSMM	muscle
50	chr11:73100800-73115800	Weak transcription	HMEC	breast

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