Variant report

Variant	rs13431704
Chromosome Location	chr2:11721816-11721817
allele	A/G
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	CTCF	chr2:11721671-11723784	SK-N-SH	brain:	n/a	chr2:11723015-11723028 chr2:11723019-11723028 chr2:11723013-11723031 chr2:11723018-11723031
2	POLR2A	chr2:11720876-11723810	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:11712005-11732311	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:11721389-11723390	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:11721360-11721911	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:11721551-11723534	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11603362..11606235-chr2:11721307..11722815,2	K562	blood:
2	chr2:11619147..11621466-chr2:11720727..11723071,2	K562	blood:

Variant related genes	Relation type
RN7SL674P	TF binding region
ENSG00000269074	Chromatin interaction
ENSG00000169016	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10174816	1.00[CEU][hapmap]
rs11681838	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11688915	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11689869	0.85[ASN][1000 genomes]
rs11886664	1.00[CEU][hapmap]
rs11895768	1.00[CEU][hapmap]
rs13421766	1.00[CEU][hapmap]
rs13432243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435547	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16857649	1.00[CEU][hapmap]
rs16857699	1.00[CEU][hapmap]
rs1865575	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2252958	1.00[CHD][hapmap]
rs2304399	1.00[CHD][hapmap]
rs36030386	1.00[ASN][1000 genomes]
rs4387757	1.00[CEU][hapmap]
rs4669756	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs62118318	0.85[ASN][1000 genomes]
rs6432217	1.00[CEU][hapmap]
rs6432218	1.00[CEU][hapmap]
rs6712902	1.00[CEU][hapmap]
rs6735957	1.00[CHD][hapmap]
rs6736604	1.00[ASN][1000 genomes]
rs6740248	1.00[CEU][hapmap]
rs6744817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745921	1.00[CEU][hapmap]
rs6757729	1.00[CEU][hapmap]
rs7557063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7559835	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7562399	1.00[CEU][hapmap]
rs7565382	1.00[CEU][hapmap]
rs7576944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7585718	1.00[CEU][hapmap]
rs7596162	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7608777	1.00[CEU][hapmap]
rs880858	1.00[ASN][1000 genomes]
rs9287733	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:11699800-11723000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
8	chr2:11700200-11723000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:11702800-11722400	Strong transcription	HepG2	liver
10	chr2:11707800-11722200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:11709800-11724200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:11710000-11722600	Weak transcription	Pancreas	Pancrea
13	chr2:11711600-11723200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
15	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:11714600-11722800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:11715600-11722200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:11716600-11722000	Strong transcription	Fetal Stomach	stomach
19	chr2:11716600-11722400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:11716600-11722400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:11717200-11722000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
23	chr2:11719000-11722800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:11719000-11723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:11719000-11723000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:11719200-11725800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:11719800-11722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:11719800-11722600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:11719800-11723000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:11720400-11722000	Enhancers	Fetal Lung	lung
34	chr2:11720400-11722800	Genic enhancers	Ovary	ovary
35	chr2:11720600-11722000	Strong transcription	Brain Substantia Nigra	brain
36	chr2:11720600-11722800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:11720800-11722000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:11720800-11722200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr2:11721000-11722200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:11721000-11722600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:11721200-11723000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:11721400-11722600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:11721800-11722000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr2:11721800-11726000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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