Variant report

Variant	rs6756691
Chromosome Location	chr2:99375800-99375801
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99374384..99376088-chr2:99411488..99413627,2	MCF-7	breast:
2	chr2:99373556..99376525-chr2:99380957..99383343,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11899659	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12464562	0.93[EUR][1000 genomes]
rs13012495	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1877905	0.82[CHB][hapmap]
rs34091873	0.82[EUR][1000 genomes]
rs34852807	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6711574	0.84[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6756691	ARID5A	cis	cerebellum	SCAN
rs6756691	RFX8	cis	parietal	SCAN
rs6756691	MGAT4A	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99372200-99380800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:99373400-99378600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:99373600-99377800	Enhancers	HUVEC	blood vessel
4	chr2:99373600-99378400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr2:99373600-99378800	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:99373800-99376800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:99373800-99378800	Enhancers	Fetal Thymus	thymus
8	chr2:99373800-99388000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:99374000-99377400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:99374000-99378000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:99374600-99376200	Enhancers	Primary B cells from cord blood	blood
12	chr2:99374600-99378200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:99374600-99383000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:99374600-99383200	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:99374800-99375800	Enhancers	GM12878-XiMat	blood
16	chr2:99374800-99376400	Weak transcription	Lung	lung
17	chr2:99374800-99376600	Weak transcription	Esophagus	oesophagus
18	chr2:99374800-99376600	Weak transcription	Pancreas	Pancrea
19	chr2:99374800-99378200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:99374800-99378800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:99374800-99378800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:99374800-99379000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:99374800-99379000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:99374800-99379000	Weak transcription	Right Atrium	heart
25	chr2:99374800-99379200	Weak transcription	Left Ventricle	heart
26	chr2:99374800-99379400	Weak transcription	Colonic Mucosa	Colon
27	chr2:99374800-99381000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:99374800-99381400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr2:99374800-99382000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:99375000-99376400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:99375000-99376600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:99375000-99377600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:99375000-99377600	Enhancers	Primary T cells from cord blood	blood
34	chr2:99375000-99378000	Weak transcription	Adipose Nuclei	Adipose
35	chr2:99375000-99378600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:99375000-99379400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:99375200-99376400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr2:99375200-99376600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:99375200-99376800	Weak transcription	HMEC	breast
40	chr2:99375200-99377600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:99375200-99377600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:99375200-99377800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:99375200-99377800	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:99375200-99378600	Enhancers	Dnd41	blood
45	chr2:99375200-99379400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:99375200-99381000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:99375200-99386200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:99375200-99386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:99375400-99376200	Enhancers	Thymus	Thymus
50	chr2:99375400-99376800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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