Variant report

Variant	rs1596116
Chromosome Location	chr4:77151474-77151475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77132958..77141575-chr4:77150872..77159587,22	MCF-7	breast:
2	chr4:77143025..77144771-chr4:77149796..77152132,2	MCF-7	breast:
3	chr4:77149994..77152737-chr4:77153466..77157199,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189157	Chromatin interaction
ENSG00000138760	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10004443	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097313	0.82[JPT][hapmap]
rs11531413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643198	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12643261	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs13114306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13117238	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs13122345	0.81[JPT][hapmap]
rs13136819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137733	0.86[JPT][hapmap]
rs13140675	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150767	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441910	0.81[JPT][hapmap]
rs1441914	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1441920	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1583943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588214	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596117	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17236158	0.82[JPT][hapmap]
rs17308336	0.82[JPT][hapmap]
rs1828138	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837867	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1876536	0.82[JPT][hapmap]
rs1876539	0.81[JPT][hapmap]
rs1948997	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2869864	0.82[JPT][hapmap]
rs34385906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34846125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35472515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35507310	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36031249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36121867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733250	0.81[JPT][hapmap]
rs4321663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859434	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4859436	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859437	0.90[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4859635	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4859641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859642	0.86[ASN][1000 genomes]
rs4859643	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4859646	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4859648	0.90[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56896076	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60225905	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817492	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6817956	0.86[ASN][1000 genomes]
rs6823078	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6846983	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6851219	0.81[JPT][hapmap]
rs71607345	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1596116	FAM47E	cis	parietal	SCAN
rs1596116	FAM47E	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77138800-77155200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:77142400-77154800	Weak transcription	Pancreas	Pancrea
3	chr4:77150200-77154400	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:77150400-77152000	ZNF genes & repeats	NHEK	skin
5	chr4:77150600-77151600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:77150600-77152200	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr4:77150600-77152400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr4:77150600-77152400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:77150600-77152600	ZNF genes & repeats	K562	blood
10	chr4:77150600-77153200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:77150800-77151600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:77151000-77151600	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr4:77151000-77154200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:77151000-77154200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:77151000-77154400	Weak transcription	Placenta	Placenta
16	chr4:77151200-77154000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:77151400-77152400	Weak transcription	Fetal Intestine Large	intestine
18	chr4:77151400-77152600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:77151400-77154200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:77151400-77154400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links