Variant report

Variant	rs1077473
Chromosome Location	chr7:4175508-4175509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:4168747..4171679-chr7:4175330..4177185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146555	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10244024	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs10265630	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1062213	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs17825860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2342505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2428875	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2527829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4723416	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4723418	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723419	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723420	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582046	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs593997	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs595545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs622731	0.87[ASN][1000 genomes]
rs622817	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs625405	0.88[JPT][hapmap]
rs640406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs660802	0.80[ASN][1000 genomes]
rs660834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs686162	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1033687	chr7:4006020-4267871	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538688	chr7:4006020-4267871	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv917252	chr7:4017819-4374090	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv527624	chr7:4027536-4424054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv869540	chr7:4063875-4302040	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv1016507	chr7:4105420-4255439	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv538691	chr7:4105420-4255439	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv2755976	chr7:4116507-4207997	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv518299	chr7:4116665-4286597	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv538692	chr7:4139994-4265562	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv887339	chr7:4161793-4223652	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv949581	chr7:4166659-4485938	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv887340	chr7:4167991-4263659	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv1820543	chr7:4167991-4286597	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv887341	chr7:4167991-4298625	Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv433015	chr7:4173613-4229445	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv981423	chr7:4173763-4177820	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1077473	ELFN1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4132400-4180200	Weak transcription	Colon Smooth Muscle	Colon
2	chr7:4154600-4191600	Weak transcription	Gastric	stomach
3	chr7:4164000-4184000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:4165600-4185800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:4167000-4176600	Strong transcription	Aorta	Aorta
6	chr7:4167000-4177200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:4167600-4181400	Weak transcription	Esophagus	oesophagus
8	chr7:4169200-4228200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:4170200-4184200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:4170800-4179000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:4171200-4175600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:4172600-4176200	Strong transcription	Spleen	Spleen
13	chr7:4172800-4183800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:4173200-4176600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr7:4173200-4176600	Enhancers	Fetal Brain Male	brain
16	chr7:4173600-4177200	Enhancers	Ovary	ovary
17	chr7:4174200-4175800	Enhancers	HepG2	liver
18	chr7:4174400-4176200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr7:4174400-4176600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:4174400-4176600	Genic enhancers	Pancreas	Pancrea
21	chr7:4175000-4176400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr7:4175000-4176400	Weak transcription	Brain Germinal Matrix	brain
23	chr7:4175000-4176600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:4175000-4177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:4175000-4178000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:4175000-4184000	Weak transcription	Fetal Intestine Large	intestine
27	chr7:4175200-4175600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr7:4175200-4176000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:4175200-4176000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:4175200-4176200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr7:4175200-4176400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr7:4175200-4176800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:4175200-4177000	Strong transcription	Fetal Intestine Small	intestine
34	chr7:4175200-4179400	Weak transcription	Fetal Lung	lung
35	chr7:4175200-4179600	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:4175400-4175600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:4175400-4175600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr7:4175400-4176000	Strong transcription	Fetal Stomach	stomach
39	chr7:4175400-4176200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr7:4175400-4176200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr7:4175400-4176400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr7:4175400-4176600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr7:4175400-4184200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links