Variant report

Variant	rs11927625
Chromosome Location	chr3:121418765-121418766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121417372..121420493-chr3:121467097..121470141,4	K562	blood:
2	chr3:121417854..121420828-chr3:121422749..121424314,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10934555	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1128154	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs1128158	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11915822	0.86[YRI][hapmap]
rs11919421	0.86[YRI][hapmap]
rs1492178	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs1919554	0.86[YRI][hapmap]
rs1919556	0.86[YRI][hapmap]
rs2070178	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2141488	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs2331812	0.81[EUR][1000 genomes]
rs3772129	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3966068	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438644	0.87[EUR][1000 genomes]
rs6770842	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs6798575	0.86[YRI][hapmap]
rs6804322	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73179962	0.87[EUR][1000 genomes]
rs73179967	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7356043	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818194	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818402	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9841861	0.81[CHB][hapmap]
rs9846174	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9849087	0.81[CHB][hapmap]
rs9859243	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9873644	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873648	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883663	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9968051	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11927625	GOLGB1	cis	Cerebellum	GTEx
rs11927625	IQCB1	cis	parietal	SCAN
rs11927625	GOLGB1	cis	Frontal Cortex	GTEx
rs11927625	HCLS1	cis	lymphoblastoid	seeQTL
rs11927625	HCLS1	cis	Lymphoblastoid	GTEx
rs11927625	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs11927625	HEG1	cis	parietal	SCAN
rs11927625	GOLGB1	cis	Temporal Cortex	GTEx
rs11927625	IQCB1	cis	cerebellum	SCAN
rs11927625	HCLS1	cis	multi-tissue	Pritchard
rs11927625	GOLGB1	cis	Brain Pons	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121425400	Weak transcription	Pancreas	Pancrea
4	chr3:121399000-121426400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:121399000-121440400	Weak transcription	K562	blood
6	chr3:121401200-121429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:121401200-121434000	Weak transcription	Gastric	stomach
8	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:121407400-121429400	Weak transcription	Esophagus	oesophagus
10	chr3:121408200-121422400	Strong transcription	Placenta	Placenta
11	chr3:121408200-121428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:121408400-121421000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:121408400-121421600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:121408600-121420400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:121408600-121421400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:121408600-121421600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:121408600-121421600	Strong transcription	Primary T cells from cord blood	blood
18	chr3:121408600-121421800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:121408600-121421800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:121408600-121422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:121408600-121424600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:121408600-121424800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:121408600-121424800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:121408600-121427400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:121408600-121428200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:121408800-121422800	Strong transcription	Primary B cells from cord blood	blood
27	chr3:121408800-121424800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:121409000-121421800	Strong transcription	HSMM	muscle
29	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:121410800-121424400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:121411000-121421200	Strong transcription	GM12878-XiMat	blood
32	chr3:121411000-121432000	Weak transcription	NHEK	skin
33	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
34	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:121411400-121432800	Weak transcription	Colonic Mucosa	Colon
36	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
37	chr3:121411600-121419200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:121412200-121423200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:121412800-121421200	Strong transcription	HepG2	liver
40	chr3:121413000-121421600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:121413600-121421400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:121414200-121428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:121414600-121422400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:121414800-121421400	Strong transcription	NHDF-Ad	bronchial
46	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
47	chr3:121415000-121419400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:121415200-121419200	Strong transcription	Osteobl	bone
49	chr3:121415200-121422600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:121415200-121422600	Strong transcription	Fetal Intestine Large	intestine

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