Variant report

Variant	rs1259356
Chromosome Location	chr12:31737992-31737993
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	POLR2A	chr12:31737848-31743421	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31733749..31740034-chr12:31741014..31744449,13	K562	blood:
2	chr12:31735394..31738773-chr12:31741793..31744223,3	MCF-7	breast:
3	chr12:31730582..31735738-chr12:31737602..31740641,5	K562	blood:

Variant related genes	Relation type
DENND5B-AS1	TF binding region
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1012154	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs10743757	0.81[CHB][hapmap]
rs10771832	0.86[CHB][hapmap]
rs10843947	0.86[CHB][hapmap]
rs11051418	0.86[CHB][hapmap]
rs11051441	0.81[CHB][hapmap]
rs11051456	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150942	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150943	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150945	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150950	0.88[AFR][1000 genomes]
rs1150953	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1150954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150963	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259233	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259235	0.91[CEU][hapmap];0.93[CHB][hapmap];0.85[YRI][hapmap]
rs1259241	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259353	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259354	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1259389	0.88[ASN][1000 genomes]
rs1259395	0.91[EUR][1000 genomes]
rs1259405	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259422	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1259426	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259428	0.81[CHB][hapmap]
rs1259430	0.84[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1259435	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259438	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259441	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1262390	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1271663	0.92[AFR][1000 genomes]
rs1272773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469673	0.86[CHB][hapmap]
rs1542536	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1677154	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1677186	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677187	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677189	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1677217	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716194	0.88[ASN][1000 genomes]
rs1716210	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716216	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2061761	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116704	0.86[CHB][hapmap]
rs2568884	0.93[CHB][hapmap]
rs2568885	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568887	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2604052	0.98[ASN][1000 genomes]
rs2617178	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617191	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2617200	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2682671	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682674	0.86[ASN][1000 genomes]
rs2682677	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682679	0.86[ASN][1000 genomes]
rs2682680	0.83[ASN][1000 genomes]
rs2682695	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682697	0.84[CHB][hapmap]
rs3850965	0.81[CHB][hapmap]
rs3898368	0.86[CHB][hapmap]
rs4312145	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482118	0.81[CHB][hapmap]
rs4931501	0.81[CHB][hapmap]
rs4931507	0.81[CHB][hapmap]
rs6487992	0.81[CHB][hapmap]
rs708200	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs708209	0.86[CHB][hapmap]
rs708212	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs708217	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7133082	0.81[CHB][hapmap]
rs7135856	0.81[CHB][hapmap]
rs7294574	0.86[CHB][hapmap]
rs7302698	0.86[CHB][hapmap]
rs7307616	0.81[CHB][hapmap]
rs7313118	0.81[CHB][hapmap]
rs793148	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793149	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793150	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793158	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793161	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs793171	0.91[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs793173	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793175	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793176	0.92[CHB][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs793177	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954595	0.81[CHB][hapmap]
rs7959877	0.86[CHB][hapmap]
rs7962896	0.86[CHB][hapmap]
rs7974437	0.81[CHB][hapmap]
rs7975761	0.86[CHB][hapmap]
rs7976644	0.86[CHB][hapmap]
rs899159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs976874	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
2	chr12:31726400-31742000	Weak transcription	Fetal Intestine Large	intestine
3	chr12:31726600-31738000	Weak transcription	Liver	Liver
4	chr12:31727000-31738000	Weak transcription	Small Intestine	intestine
5	chr12:31728000-31741000	Weak transcription	Right Ventricle	heart
6	chr12:31728200-31738000	Weak transcription	Hela-S3	cervix
7	chr12:31728400-31741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:31728800-31738200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:31728800-31738200	Weak transcription	HepG2	liver
10	chr12:31730800-31738200	Weak transcription	Primary B cells from cord blood	blood
11	chr12:31732000-31738000	Weak transcription	NHLF	lung
12	chr12:31732000-31741400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:31732200-31738200	Weak transcription	Brain Angular Gyrus	brain
14	chr12:31732200-31738200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:31732200-31738200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:31732200-31741600	Weak transcription	Fetal Kidney	kidney
17	chr12:31732400-31738000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:31732400-31738200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:31732400-31741000	Weak transcription	Pancreas	Pancrea
20	chr12:31735000-31738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:31735400-31738000	Weak transcription	NH-A	brain
22	chr12:31735400-31738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:31735600-31738000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:31735600-31738000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:31735800-31738000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:31735800-31738000	Weak transcription	NHEK	skin
27	chr12:31735800-31739800	Weak transcription	Spleen	Spleen
28	chr12:31736600-31738000	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:31736600-31738200	Enhancers	A549	lung
30	chr12:31736600-31738600	Enhancers	HUVEC	blood vessel
31	chr12:31736800-31740000	Enhancers	Fetal Heart	heart
32	chr12:31737000-31738000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:31737000-31738600	Enhancers	Fetal Muscle Leg	muscle
34	chr12:31737000-31738800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:31737000-31738800	Enhancers	Ovary	ovary
36	chr12:31737000-31739400	Enhancers	HSMMtube	muscle
37	chr12:31737200-31738200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:31737200-31738600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:31737200-31738800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr12:31737200-31738800	Enhancers	Brain Anterior Caudate	brain
41	chr12:31737200-31738800	Enhancers	Brain Hippocampus Middle	brain
42	chr12:31737200-31739000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr12:31737200-31739000	Enhancers	Stomach Mucosa	stomach
44	chr12:31737400-31738200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:31737400-31738200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:31737400-31738400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:31737400-31738600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr12:31737400-31738600	Enhancers	Psoas Muscle	Psoas
49	chr12:31737400-31738800	Enhancers	Left Ventricle	heart
50	chr12:31737400-31741000	Weak transcription	Brain Germinal Matrix	brain

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