Variant report

Variant	rs6439629
Chromosome Location	chr3:135901270-135901271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135898599..135901770-chr3:135904262..135906651,3	K562	blood:
2	chr3:135900499..135903369-chr3:135912979..135914958,2	K562	blood:
3	chr3:135899797..135903153-chr3:135915124..135917007,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10512990	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12330335	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12695644	0.81[AMR][1000 genomes]
rs13068210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13079205	1.00[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13081671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082532	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1393786	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1393787	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1403763	1.00[CEU][hapmap]
rs2305265	1.00[CHB][hapmap]
rs28519617	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28535121	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28669017	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34324561	0.80[AFR][1000 genomes]
rs34864445	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35320690	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35352346	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3732519	1.00[CHB][hapmap]
rs3732521	1.00[CHB][hapmap]
rs3821444	1.00[CHB][hapmap]
rs3905668	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56398805	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67109185	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67589653	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6769762	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6771253	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6775778	0.95[CEU][hapmap]
rs6786532	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6786582	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6792630	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793835	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6799056	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6799503	0.81[ASN][1000 genomes]
rs73222243	0.88[EUR][1000 genomes]
rs9653930	1.00[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9826454	0.89[AFR][1000 genomes]
rs9827662	0.89[CEU][hapmap]
rs9834966	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9837158	1.00[YRI][hapmap]
rs9848926	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9870122	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9881400	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135862000-135904800	Weak transcription	Hela-S3	cervix
2	chr3:135871200-135905000	Weak transcription	Fetal Stomach	stomach
3	chr3:135872800-135903600	Weak transcription	Thymus	Thymus
4	chr3:135880000-135906600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:135882800-135905200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:135883400-135901800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:135889200-135905000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:135889400-135907000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:135889400-135910400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:135889800-135905000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:135890000-135903800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:135890400-135905000	Weak transcription	NHDF-Ad	bronchial
13	chr3:135890400-135909600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:135891000-135905000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:135891400-135904200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:135893600-135904800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:135893600-135905000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:135893600-135910400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:135894400-135906800	Weak transcription	Esophagus	oesophagus
20	chr3:135895400-135907000	Weak transcription	Fetal Brain Male	brain
21	chr3:135895800-135901400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:135896400-135905200	Weak transcription	Fetal Intestine Small	intestine
23	chr3:135896800-135901600	Enhancers	Primary T cells from cord blood	blood
24	chr3:135897000-135904800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:135897400-135907600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:135897400-135909800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr3:135897600-135909000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:135897600-135911000	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:135898000-135910200	Weak transcription	HSMM	muscle
30	chr3:135898400-135901400	Weak transcription	Psoas Muscle	Psoas
31	chr3:135898400-135901600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:135898400-135909200	Weak transcription	Aorta	Aorta
33	chr3:135898600-135904800	Weak transcription	Stomach Mucosa	stomach
34	chr3:135898800-135901400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:135898800-135901400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:135898800-135901400	Weak transcription	Left Ventricle	heart
37	chr3:135898800-135901400	Weak transcription	Right Ventricle	heart
38	chr3:135898800-135902200	Weak transcription	Ovary	ovary
39	chr3:135898800-135904400	Weak transcription	Lung	lung
40	chr3:135898800-135905000	Weak transcription	Gastric	stomach
41	chr3:135898800-135905200	Weak transcription	Fetal Thymus	thymus
42	chr3:135898800-135905200	Weak transcription	Pancreas	Pancrea
43	chr3:135898800-135907000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:135899000-135905200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:135899800-135902000	Enhancers	Small Intestine	intestine
46	chr3:135900000-135901600	Enhancers	NHEK	skin
47	chr3:135900000-135902800	Enhancers	A549	lung
48	chr3:135900000-135904600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:135900000-135905200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:135900200-135901400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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