Variant report

Variant	rs3798558
Chromosome Location	chr6:34326003-34326004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34324031..34326869-chr6:34337955..34340414,2	K562	blood:
2	chr6:34290820..34292896-chr6:34325616..34327801,2	K562	blood:
3	chr6:34320498..34323149-chr6:34325939..34328541,3	K562	blood:
4	chr6:34203217..34204857-chr6:34324841..34327687,2	MCF-7	breast:
5	chr6:34325579..34328328-chr6:34358268..34360941,3	K562	blood:

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10484267	1.00[YRI][hapmap]
rs10484268	1.00[YRI][hapmap]
rs1057691	1.00[YRI][hapmap]
rs1060308	1.00[YRI][hapmap]
rs10648	1.00[YRI][hapmap]
rs1265	1.00[YRI][hapmap]
rs13466	1.00[YRI][hapmap]
rs16883137	1.00[YRI][hapmap]
rs16883475	1.00[YRI][hapmap]
rs17628946	1.00[YRI][hapmap]
rs17629180	1.00[YRI][hapmap]
rs17629270	1.00[YRI][hapmap]
rs17696583	1.00[YRI][hapmap]
rs17696774	1.00[YRI][hapmap]
rs17696829	1.00[YRI][hapmap]
rs34213452	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734363	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798557	1.00[YRI][hapmap]
rs59799357	1.00[ASN][1000 genomes]
rs7764733	1.00[CHB][hapmap]
rs875274	1.00[YRI][hapmap]

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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34285200-34330600	Weak transcription	Thymus	Thymus
3	chr6:34285800-34326600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:34298600-34326400	Weak transcription	A549	lung
5	chr6:34306000-34327800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:34306000-34328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:34308800-34330800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:34309600-34329200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:34309800-34327000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:34309800-34329800	Weak transcription	Fetal Thymus	thymus
11	chr6:34309800-34330800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:34309800-34337600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:34309800-34347200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:34310000-34330600	Weak transcription	Dnd41	blood
15	chr6:34310400-34329200	Weak transcription	Brain Angular Gyrus	brain
16	chr6:34310600-34326400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:34310800-34330800	Weak transcription	Primary T cells from cord blood	blood
18	chr6:34315400-34351200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:34316200-34333400	Weak transcription	Placenta	Placenta
20	chr6:34317400-34330800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:34318200-34326400	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:34318200-34330600	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:34318200-34355800	Weak transcription	Brain Germinal Matrix	brain
24	chr6:34318400-34330000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:34318600-34330600	Weak transcription	Fetal Intestine Small	intestine
26	chr6:34318800-34327400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:34318800-34330600	Weak transcription	Adipose Nuclei	Adipose
28	chr6:34319400-34327600	Weak transcription	Right Atrium	heart
29	chr6:34320200-34327600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:34320200-34330800	Weak transcription	Primary B cells from cord blood	blood
31	chr6:34320400-34326400	Weak transcription	Ovary	ovary
32	chr6:34320400-34330400	Weak transcription	Aorta	Aorta
33	chr6:34320400-34330800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:34320400-34330800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:34320400-34333400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:34320400-34350400	Weak transcription	Esophagus	oesophagus
37	chr6:34320600-34326400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:34320600-34326400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:34320600-34326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:34320600-34326400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:34320600-34327600	Weak transcription	Fetal Stomach	stomach
42	chr6:34320600-34330600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:34320600-34331000	Weak transcription	Small Intestine	intestine
44	chr6:34320800-34326200	Weak transcription	NHLF	lung
45	chr6:34321000-34327200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:34321200-34326400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:34321200-34327200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:34321600-34327200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:34321600-34328800	Weak transcription	GM12878-XiMat	blood
50	chr6:34322200-34326400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links