Variant report

Variant	rs7950873
Chromosome Location	chr11:77412851-77412852
allele	A/C/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	chr11:77412754-77412899	ProgFib	skin:	n/a	n/a

Variant related genes	Relation type
RSF1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10899394	0.88[TSI][hapmap]
rs10899399	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10899404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11237244	0.85[GIH][hapmap];0.82[TSI][hapmap]
rs11237249	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs11237263	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11237280	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11600998	0.86[ASN][1000 genomes]
rs11603438	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11604207	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs12286317	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17752006	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2032395	0.82[TSI][hapmap]
rs2154972	0.84[EUR][1000 genomes]
rs24356	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2508189	0.82[EUR][1000 genomes]
rs34130561	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4322421	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4344516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs484363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4945220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs537811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56218634	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs588217	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs614495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs621456	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs623173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs623907	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs643388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs648601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs648896	0.86[AFR][1000 genomes]
rs650171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs663674	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[TSI][hapmap]
rs668701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs684813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs687037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs695046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[TSI][hapmap]
rs7122968	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7123080	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs72945592	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72945598	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72947625	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72947668	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72949616	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72949618	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7951033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs947841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer 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 target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
6	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv468641	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv555452	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1035494	chr11:77309696-77431228	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7950873	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs7950873	INTS4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77360400-77419200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:77373800-77413600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:77374000-77416200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:77374200-77417400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:77374800-77414000	Strong transcription	Fetal Thymus	thymus
6	chr11:77375000-77413000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:77375200-77413600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:77375600-77413200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:77375600-77413400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:77376800-77415600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr11:77386400-77414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:77387200-77416600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:77388000-77413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:77388000-77413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:77388600-77415800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:77389400-77413400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:77389800-77435400	Weak transcription	Psoas Muscle	Psoas
18	chr11:77391600-77442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:77394200-77425200	Weak transcription	Lung	lung
20	chr11:77394600-77416600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:77394600-77435600	Weak transcription	Gastric	stomach
22	chr11:77394600-77441800	Weak transcription	Spleen	Spleen
23	chr11:77394600-77445600	Weak transcription	Esophagus	oesophagus
24	chr11:77394600-77458800	Weak transcription	Small Intestine	intestine
25	chr11:77394800-77418200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:77394800-77462600	Weak transcription	Fetal Heart	heart
27	chr11:77398800-77422400	Weak transcription	Pancreas	Pancrea
28	chr11:77400200-77413400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:77402200-77416800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:77402600-77435800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:77403200-77442200	Weak transcription	Brain Anterior Caudate	brain
32	chr11:77404600-77441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:77405000-77415000	Weak transcription	Fetal Intestine Small	intestine
34	chr11:77405600-77413800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:77406400-77434600	Weak transcription	Fetal Brain Female	brain
36	chr11:77406800-77428000	Weak transcription	Ovary	ovary
37	chr11:77407000-77413200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:77407200-77448000	Weak transcription	K562	blood
39	chr11:77408400-77434200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:77409400-77441600	Weak transcription	Brain Hippocampus Middle	brain
41	chr11:77409600-77414800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:77409600-77415000	Weak transcription	Fetal Lung	lung
43	chr11:77409600-77415000	Weak transcription	Right Ventricle	heart
44	chr11:77409600-77415200	Weak transcription	Fetal Kidney	kidney
45	chr11:77409600-77415600	Weak transcription	HMEC	breast
46	chr11:77409600-77416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:77409600-77428000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:77409600-77432600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:77409600-77435200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:77409600-77435400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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