Variant report

Variant	rs1178014
Chromosome Location	chr2:172204357-172204358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172181378..172183411-chr2:172203643..172205572,2	K562	blood:
2	chr2:172202384..172205221-chr2:172288983..172291162,2	MCF-7	breast:
3	chr2:172203360..172205548-chr2:172289457..172291290,2	K562	blood:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10173812	0.92[EUR][1000 genomes]
rs11674303	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685308	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11695531	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12327994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989804	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3731986	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731987	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6744452	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7349355	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888521	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:172181000-172221600	Weak transcription	K562	blood
4	chr2:172193600-172218200	Weak transcription	HepG2	liver
5	chr2:172202200-172212200	Weak transcription	Esophagus	oesophagus
6	chr2:172202400-172211800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:172202600-172204600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr2:172202600-172204600	Enhancers	HUVEC	blood vessel
9	chr2:172202800-172204400	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:172202800-172204600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:172202800-172204800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:172203000-172204400	Flanking Active TSS	GM12878-XiMat	blood
13	chr2:172203000-172204400	Enhancers	HSMMtube	muscle
14	chr2:172203000-172204600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr2:172203000-172204600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:172203000-172205000	Enhancers	NHLF	lung
17	chr2:172203200-172204600	Enhancers	Fetal Thymus	thymus
18	chr2:172203200-172205000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:172203200-172205000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:172203200-172205000	Enhancers	Fetal Muscle Leg	muscle
21	chr2:172203200-172205200	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:172203400-172204400	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:172203400-172204400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:172203400-172204400	Enhancers	Thymus	Thymus
25	chr2:172203400-172204600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:172203400-172204600	Enhancers	Fetal Heart	heart
27	chr2:172203400-172205000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:172203400-172205000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:172203400-172205000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:172203400-172205000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:172203400-172205000	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:172203400-172205200	Enhancers	Colon Smooth Muscle	Colon
33	chr2:172203400-172217200	Weak transcription	Small Intestine	intestine
34	chr2:172203600-172204400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:172203600-172204800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:172203600-172204800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:172203600-172204800	Enhancers	Fetal Stomach	stomach
38	chr2:172203600-172204800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:172203600-172205000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:172203600-172205000	Enhancers	A549	lung
41	chr2:172203600-172205000	Enhancers	Osteobl	bone
42	chr2:172203600-172205200	Enhancers	NHDF-Ad	bronchial
43	chr2:172203800-172204400	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr2:172203800-172204600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:172203800-172204600	Flanking Active TSS	NH-A	brain
46	chr2:172203800-172204800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr2:172203800-172205000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:172203800-172205000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:172203800-172205200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:172203800-172205600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links