Variant report

Variant	rs836556
Chromosome Location	chr7:6447041-6447042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6445380..6448087-chr7:6488948..6490884,2	K562	blood:
2	chr7:6444358..6447267-chr7:6449792..6451395,2	K562	blood:
3	chr7:6439883..6442472-chr7:6446934..6449638,2	MCF-7	breast:
4	chr7:6413088..6415412-chr7:6446957..6448818,2	MCF-7	breast:
5	chr7:6446943..6448782-chr7:6451434..6453838,3	K562	blood:
6	chr7:6442339..6447267-chr7:6447321..6451395,5	K562	blood:

Variant related genes	Relation type
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10281392	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs12112106	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs13238780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2689420	0.81[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs4724798	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs702483	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs702485	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs702486	0.92[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73057348	0.97[ASN][1000 genomes]
rs755629	0.81[CHB][hapmap]
rs836471	0.84[EUR][1000 genomes]
rs836477	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836478	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836480	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836483	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836487	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs836489	0.82[ASN][1000 genomes]
rs836494	0.85[ASN][1000 genomes]
rs836498	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs836499	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836503	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs836508	0.92[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs836509	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs836513	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836516	0.92[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs836521	0.81[EUR][1000 genomes]
rs836526	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836527	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836529	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836534	0.92[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs836536	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836539	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836549	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs836551	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs836558	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836559	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861369	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs866278	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv605999	chr7:6396719-6472881	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv606000	chr7:6446027-6477002	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs836556	MGC12966	cis	multi-tissue	Pritchard
rs836556	RPA3	cis	cerebellum	SCAN
rs836556	RAC1	Cis_1M	lymphoblastoid	RTeQTL
rs836556	LOC221955	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6426000-6456400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:6426000-6475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:6426400-6457400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6436200-6448200	Weak transcription	Small Intestine	intestine
5	chr7:6437200-6449000	Strong transcription	Fetal Stomach	stomach
6	chr7:6437400-6457400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:6437400-6457400	Strong transcription	Dnd41	blood
8	chr7:6437600-6470400	Strong transcription	Fetal Brain Female	brain
9	chr7:6437800-6450200	Strong transcription	Thymus	Thymus
10	chr7:6437800-6456400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:6437800-6457200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr7:6437800-6457400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr7:6438000-6457400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr7:6438000-6458000	Strong transcription	Osteobl	bone
15	chr7:6438000-6462400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:6438200-6450600	Strong transcription	Colonic Mucosa	Colon
17	chr7:6438600-6457200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:6438600-6457400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:6438600-6475600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:6438800-6457400	Strong transcription	Primary T cells from cord blood	blood
21	chr7:6438800-6457600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:6438800-6462800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr7:6439000-6456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:6439200-6456000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:6439200-6456800	Strong transcription	NHDF-Ad	bronchial
26	chr7:6439200-6457200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:6439200-6457400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:6439400-6448800	Strong transcription	Fetal Intestine Large	intestine
29	chr7:6439400-6454200	Strong transcription	Spleen	Spleen
30	chr7:6439400-6457200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:6439400-6457400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr7:6439400-6457400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr7:6439400-6458000	Strong transcription	Fetal Muscle Leg	muscle
34	chr7:6439600-6447200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:6439600-6449400	Weak transcription	Psoas Muscle	Psoas
36	chr7:6439600-6456000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr7:6439600-6456600	Strong transcription	HUVEC	blood vessel
38	chr7:6439600-6456800	Strong transcription	Aorta	Aorta
39	chr7:6439600-6457000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:6439600-6457000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:6439600-6457200	Strong transcription	Fetal Lung	lung
42	chr7:6439600-6457400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:6439600-6472400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:6439800-6454800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr7:6439800-6457400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:6439800-6457400	Strong transcription	Liver	Liver
47	chr7:6439800-6457400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr7:6439800-6474600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:6439800-6474600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:6439800-6477400	Strong transcription	Fetal Intestine Small	intestine

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