Variant report

Variant	rs836480
Chromosome Location	chr7:6431404-6431405
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6412666..6416399-chr7:6429961..6432840,4	MCF-7	breast:
2	chr7:6413960..6415587-chr7:6430551..6433223,4	K562	blood:
3	chr7:6425039..6427961-chr7:6431283..6434070,6	K562	blood:

Variant related genes	Relation type
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10281392	0.82[CHB][hapmap]
rs12112106	0.82[CHB][hapmap]
rs13238780	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2689420	0.80[CEU][hapmap];0.80[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs2742122	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4724798	0.82[CHB][hapmap]
rs702483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702485	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs702486	0.85[CEU][hapmap]
rs73057348	0.87[ASN][1000 genomes]
rs755629	0.81[CHB][hapmap]
rs836471	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs836477	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836483	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836487	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836489	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836492	0.84[EUR][1000 genomes]
rs836494	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836499	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836508	0.85[CEU][hapmap]
rs836509	0.88[CEU][hapmap]
rs836513	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs836516	0.85[CEU][hapmap]
rs836526	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs836527	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs836529	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs836534	0.85[CEU][hapmap]
rs836536	0.82[ASN][1000 genomes]
rs836539	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836551	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836556	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]
rs836558	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836559	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861369	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs866278	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs836480	ICA1	cis	cerebellum	SCAN
rs836480	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6417200-6435400	Weak transcription	Fetal Brain Male	brain
2	chr7:6423000-6432400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:6424000-6432400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6424000-6432400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:6425400-6432600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:6425600-6432200	Weak transcription	Fetal Heart	heart
7	chr7:6425800-6432600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:6426000-6432400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:6426000-6432400	Weak transcription	Ovary	ovary
10	chr7:6426000-6432400	Weak transcription	Right Atrium	heart
11	chr7:6426000-6456400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:6426000-6475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:6426200-6431800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:6426400-6432400	Weak transcription	Psoas Muscle	Psoas
15	chr7:6426400-6457400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:6426600-6431800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:6426600-6432000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr7:6426600-6432400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:6426600-6432600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:6426600-6434200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:6426600-6434400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:6426600-6436200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:6426800-6432400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr7:6426800-6432400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:6426800-6432400	Strong transcription	GM12878-XiMat	blood
26	chr7:6426800-6432400	Strong transcription	HSMM	muscle
27	chr7:6426800-6432600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:6426800-6434600	Strong transcription	HepG2	liver
29	chr7:6426800-6436200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:6426800-6436400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:6426800-6436600	Strong transcription	Dnd41	blood
32	chr7:6427000-6431600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:6427000-6431800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:6427000-6432000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:6427000-6432200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr7:6427000-6432400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:6427000-6432400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:6427000-6432400	Strong transcription	Fetal Muscle Leg	muscle
39	chr7:6427000-6433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:6427000-6433000	Strong transcription	Fetal Thymus	thymus
41	chr7:6427000-6436400	Strong transcription	Fetal Stomach	stomach
42	chr7:6427200-6432400	Strong transcription	Osteobl	bone
43	chr7:6427200-6433600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:6427200-6434200	Strong transcription	Fetal Brain Female	brain
45	chr7:6427400-6432200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:6427400-6432400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:6427400-6432400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:6427400-6432400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:6427400-6432400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:6427400-6432400	Strong transcription	Thymus	Thymus

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