Variant report

Variant	rs17495838
Chromosome Location	chr11:66196265-66196266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66196233-66196869	H1-neurons	neurons:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66191998..66197542-chr11:66203958..66207660,7	K562	blood:
2	chr11:66193480..66197542-chr11:66204605..66206525,3	K562	blood:
3	chr11:66193187..66197390-chr11:66197720..66199411,3	K562	blood:
4	chr11:66175850..66176382-chr11:66195828..66196350,2	MCF-7	breast:
5	chr11:66175611..66176479-chr11:66196191..66196952,2	MCF-7	breast:
6	chr11:66188152..66192290-chr11:66193930..66197880,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000201733	TF binding region
ENSG00000174547	Chromatin interaction
ENSG00000174576	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10501397	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10896124	0.80[EUR][1000 genomes]
rs10896125	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11227495	0.81[EUR][1000 genomes]
rs11227497	0.82[EUR][1000 genomes]
rs11227498	0.82[EUR][1000 genomes]
rs11227499	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs11227500	0.82[EUR][1000 genomes]
rs11227501	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs11227502	0.82[EUR][1000 genomes]
rs11227503	0.82[EUR][1000 genomes]
rs11227509	0.82[EUR][1000 genomes]
rs11227510	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11227511	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11227512	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11227514	0.82[EUR][1000 genomes]
rs11227515	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs11227523	0.81[EUR][1000 genomes]
rs11227525	0.81[EUR][1000 genomes]
rs11227527	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11227534	1.00[CEU][hapmap]
rs11550057	1.00[LWK][hapmap]
rs11550299	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11821155	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs11822028	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11822099	0.82[EUR][1000 genomes]
rs11824771	0.81[EUR][1000 genomes]
rs12099041	0.89[EUR][1000 genomes]
rs12221821	0.82[EUR][1000 genomes]
rs13897	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs15969	1.00[LWK][hapmap]
rs17065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17147644	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs17496250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17580784	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075792	1.00[CEU][hapmap]
rs2276406	0.82[EUR][1000 genomes]
rs2277302	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2279864	0.89[EUR][1000 genomes]
rs2279865	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs2298806	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2305532	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2305533	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2305535	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3179961	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs35733139	0.91[EUR][1000 genomes]
rs3737525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3741360	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3816492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3819247	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3825065	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3867131	0.87[EUR][1000 genomes]
rs3892818	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs4542420	0.82[EUR][1000 genomes]
rs4576	1.00[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs4630309	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs4930182	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930183	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4930377	0.87[EUR][1000 genomes]
rs4930378	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4930379	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4930380	0.83[EUR][1000 genomes]
rs56144989	0.81[EUR][1000 genomes]
rs57207756	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57288351	0.81[EUR][1000 genomes]
rs57634456	0.83[EUR][1000 genomes]
rs57691879	0.89[EUR][1000 genomes]
rs57724777	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58752760	0.83[ASN][1000 genomes]
rs59982644	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60358007	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60645853	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61561111	0.81[EUR][1000 genomes]
rs61582507	0.85[EUR][1000 genomes]
rs7104378	0.95[EUR][1000 genomes]
rs7116921	0.81[EUR][1000 genomes]
rs7123176	0.80[EUR][1000 genomes]
rs7928882	1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[EUR][1000 genomes]
rs7943327	0.83[EUR][1000 genomes]
rs7950407	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7950790	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17495838	CHKA	cis	cerebellum	SCAN
rs17495838	RBM4	cis	cerebellum	SCAN
rs17495838	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs17495838	C11orf80	cis	cerebellum	SCAN
rs17495838	ASRGL1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66188800-66202600	Weak transcription	Esophagus	oesophagus
2	chr11:66188800-66205600	Weak transcription	Right Atrium	heart
3	chr11:66189000-66200200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:66189000-66200200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:66189000-66200600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:66189000-66202400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:66189000-66202600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:66189000-66204800	Weak transcription	Fetal Heart	heart
9	chr11:66189200-66200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:66189200-66200600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:66189200-66201800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:66189200-66202600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:66189200-66205600	Weak transcription	Stomach Mucosa	stomach
14	chr11:66189600-66200000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:66189800-66200000	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:66189800-66202600	Weak transcription	Brain Anterior Caudate	brain
17	chr11:66190000-66196600	Strong transcription	Fetal Stomach	stomach
18	chr11:66190000-66202800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:66190200-66202400	Weak transcription	Brain Angular Gyrus	brain
20	chr11:66190200-66202600	Weak transcription	Pancreas	Pancrea
21	chr11:66190200-66205000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:66190400-66202600	Weak transcription	Spleen	Spleen
23	chr11:66190800-66202600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr11:66191400-66200200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:66191400-66201200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:66191400-66203600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:66191600-66205600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:66191800-66202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:66192200-66199400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:66192200-66200200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:66192200-66200200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:66192200-66201000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:66192200-66204400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:66192400-66197400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:66192800-66200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:66192800-66202800	Weak transcription	Aorta	Aorta
37	chr11:66193400-66202600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:66193600-66202400	Weak transcription	Colon Smooth Muscle	Colon
39	chr11:66194000-66202600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:66194200-66202400	Weak transcription	Primary B cells from cord blood	blood
41	chr11:66194600-66199400	Weak transcription	Fetal Intestine Small	intestine
42	chr11:66194600-66200200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:66194600-66202600	Weak transcription	Lung	lung
44	chr11:66194800-66202600	Weak transcription	A549	lung
45	chr11:66195000-66201800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:66195000-66202600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:66195000-66202600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:66195000-66202800	Weak transcription	Fetal Lung	lung
49	chr11:66195200-66199200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr11:66195600-66202600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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