Variant report

Variant	rs1677189
Chromosome Location	chr12:31736724-31736725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr12:31733856..31736824-chr12:31741317..31742941,2	K562	blood:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10743757	0.80[CHB][hapmap]
rs10771832	0.86[CHB][hapmap]
rs10843947	0.86[CHB][hapmap]
rs11051418	0.85[CHB][hapmap]
rs11051441	0.80[CHB][hapmap]
rs1150942	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs1150943	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150945	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150954	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150955	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1150963	0.84[AMR][1000 genomes]
rs11615961	0.86[CHB][hapmap]
rs1259233	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259241	0.84[AMR][1000 genomes]
rs1259353	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1259354	0.84[AMR][1000 genomes]
rs1259356	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]
rs1259359	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1259386	0.83[CHB][hapmap]
rs1259395	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1259405	0.82[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1259409	0.86[CHB][hapmap]
rs1259422	0.91[AFR][1000 genomes]
rs1259426	0.91[AMR][1000 genomes]
rs1259428	0.80[CHB][hapmap]
rs1259430	0.87[YRI][hapmap]
rs1259435	0.84[AMR][1000 genomes]
rs1259437	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1259438	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1259441	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1262390	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1271663	0.83[AFR][1000 genomes]
rs1272773	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1469673	0.86[CHB][hapmap]
rs1542536	0.91[AMR][1000 genomes]
rs1677154	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1677186	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1677187	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1677217	0.90[AMR][1000 genomes]
rs1716210	0.88[AMR][1000 genomes]
rs2061761	0.80[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2116704	0.86[CHB][hapmap]
rs2568887	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs2617178	0.81[AMR][1000 genomes]
rs2617191	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2682671	0.81[AMR][1000 genomes]
rs2682679	0.84[AMR][1000 genomes]
rs2682695	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs3850965	0.80[CHB][hapmap]
rs4482118	0.80[CHB][hapmap]
rs4931501	0.80[CHB][hapmap]
rs4931507	0.80[CHB][hapmap]
rs6487992	0.80[CHB][hapmap]
rs708200	0.82[JPT][hapmap]
rs708209	0.86[CHB][hapmap]
rs708212	0.82[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs708215	0.81[AMR][1000 genomes]
rs708217	0.81[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs7133082	0.80[CHB][hapmap]
rs7135856	0.80[CHB][hapmap]
rs7136476	0.86[CHB][hapmap]
rs7294574	0.86[CHB][hapmap]
rs7302698	0.86[CHB][hapmap]
rs7307616	0.80[CHB][hapmap]
rs7313118	0.80[CHB][hapmap]
rs792875	0.81[AMR][1000 genomes]
rs793148	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs793149	0.81[AMR][1000 genomes]
rs793150	0.82[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap]
rs793158	0.81[CEU][hapmap];0.80[CHB][hapmap];0.81[AMR][1000 genomes]
rs793161	0.82[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs793173	0.87[AMR][1000 genomes]
rs793174	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs793177	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs793186	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7954595	0.80[CHB][hapmap]
rs7959877	0.86[CHB][hapmap]
rs7962896	0.86[CHB][hapmap]
rs7974437	0.80[CHB][hapmap]
rs7975761	0.86[CHB][hapmap]
rs7976644	0.86[CHB][hapmap]
rs899159	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs976874	0.87[AMR][1000 genomes];0.83[EUR][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:54 , 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	chr12:31727800-31737200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:31728000-31741000	Weak transcription	Right Ventricle	heart
7	chr12:31728200-31738000	Weak transcription	Hela-S3	cervix
8	chr12:31728400-31741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:31728800-31738200	Weak transcription	Fetal Intestine Small	intestine
10	chr12:31728800-31738200	Weak transcription	HepG2	liver
11	chr12:31729800-31737400	Weak transcription	Left Ventricle	heart
12	chr12:31730800-31738200	Weak transcription	Primary B cells from cord blood	blood
13	chr12:31731200-31736800	Weak transcription	GM12878-XiMat	blood
14	chr12:31731800-31737000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:31732000-31737000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:31732000-31737200	Weak transcription	Brain Anterior Caudate	brain
17	chr12:31732000-31737200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:31732000-31737400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:31732000-31738000	Weak transcription	NHLF	lung
20	chr12:31732000-31741400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:31732200-31737200	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:31732200-31737800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:31732200-31738200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:31732200-31738200	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:31732200-31738200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:31732200-31741600	Weak transcription	Fetal Kidney	kidney
27	chr12:31732400-31737400	Weak transcription	Psoas Muscle	Psoas
28	chr12:31732400-31738000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:31732400-31738200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:31732400-31741000	Weak transcription	Pancreas	Pancrea
31	chr12:31732600-31737000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:31732600-31737800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:31734000-31737000	Weak transcription	Ovary	ovary
34	chr12:31735000-31737400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:31735000-31738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:31735400-31737000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:31735400-31737000	Weak transcription	HSMMtube	muscle
38	chr12:31735400-31737800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:31735400-31738000	Weak transcription	NH-A	brain
40	chr12:31735400-31738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:31735600-31736800	Weak transcription	Fetal Heart	heart
42	chr12:31735600-31738000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:31735600-31738000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:31735800-31737000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:31735800-31737000	Weak transcription	HSMM	muscle
46	chr12:31735800-31737800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:31735800-31737800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:31735800-31738000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:31735800-31738000	Weak transcription	NHEK	skin
50	chr12:31735800-31739800	Weak transcription	Spleen	Spleen

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