Variant report

Variant	rs7600978
Chromosome Location	chr2:153029909-153029910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153026916..153030201-chr2:153030612..153032504,5	MCF-7	breast:
2	chr2:153028161..153030497-chr2:153166137..153168907,2	K562	blood:
3	chr2:153020830..153022927-chr2:153028823..153031292,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10166701	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181910	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10182993	1.00[ASN][1000 genomes]
rs10188437	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10190828	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202920	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203589	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209826	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693278	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13382381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390486	1.00[ASN][1000 genomes]
rs13390828	1.00[ASN][1000 genomes]
rs13394982	1.00[ASN][1000 genomes]
rs13401202	1.00[ASN][1000 genomes]
rs13408535	1.00[ASN][1000 genomes]
rs13408915	1.00[ASN][1000 genomes]
rs13408985	1.00[ASN][1000 genomes]
rs13415898	1.00[ASN][1000 genomes]
rs13416727	1.00[ASN][1000 genomes]
rs13420003	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28581765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35406869	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58932175	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59794582	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726207	1.00[ASN][1000 genomes]
rs6742020	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6742139	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6753703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590270	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7604840	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9288076	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9288079	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153000200-153031000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:153002800-153030400	Weak transcription	Thymus	Thymus
3	chr2:153015400-153030200	Weak transcription	Primary T cells from cord blood	blood
4	chr2:153017000-153030200	Weak transcription	Fetal Stomach	stomach
5	chr2:153021200-153030600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:153022200-153031400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:153022800-153031200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:153022800-153031200	Weak transcription	Gastric	stomach
9	chr2:153022800-153031200	Weak transcription	Left Ventricle	heart
10	chr2:153023400-153030400	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:153023400-153030800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:153023600-153030400	Weak transcription	HSMMtube	muscle
13	chr2:153024000-153030400	Weak transcription	Fetal Thymus	thymus
14	chr2:153024000-153030400	Weak transcription	NH-A	brain
15	chr2:153024000-153030400	Weak transcription	NHDF-Ad	bronchial
16	chr2:153024000-153030600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:153024000-153030600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:153024000-153030800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:153024000-153030800	Weak transcription	Fetal Heart	heart
20	chr2:153024000-153030800	Weak transcription	K562	blood
21	chr2:153024200-153030400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:153024200-153030400	Weak transcription	HUVEC	blood vessel
23	chr2:153024200-153031000	Weak transcription	HSMM	muscle
24	chr2:153024400-153030400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:153027600-153031200	Weak transcription	Lung	lung
26	chr2:153028000-153030400	Enhancers	Liver	Liver
27	chr2:153028000-153030800	Enhancers	Fetal Intestine Small	intestine
28	chr2:153028200-153030400	Enhancers	Dnd41	blood
29	chr2:153028200-153030800	Enhancers	Fetal Lung	lung
30	chr2:153028200-153031000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr2:153028200-153031200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:153028400-153031400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr2:153028600-153030000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:153028600-153030400	Weak transcription	Brain Angular Gyrus	brain
35	chr2:153028600-153030400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:153028600-153030400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:153028600-153030800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:153028600-153030800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:153028600-153030800	Weak transcription	Aorta	Aorta
40	chr2:153028600-153030800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:153028600-153031000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:153028800-153030200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:153028800-153030400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:153028800-153030800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:153028800-153030800	Weak transcription	Fetal Brain Male	brain
46	chr2:153028800-153031000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:153029000-153030000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:153029000-153030000	Weak transcription	Esophagus	oesophagus
49	chr2:153029000-153030000	Weak transcription	Fetal Intestine Large	intestine
50	chr2:153029000-153030000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links