Variant report

Variant	rs7516189
Chromosome Location	chr1:211828134-211828135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:211826517-211829499	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr1:211828017-211829192	SK-N-SH	brain:	n/a	chr1:211828725-211828739
3	CTCF	chr1:211828098-211829164	SK-N-SH	brain:	n/a	chr1:211828724-211828740 chr1:211828725-211828738 chr1:211828723-211828741 chr1:211828725-211828738 chr1:211828718-211828739

No.	Distal block	Cell Line	Cell type
1	chr1:211750915..211755112-chr1:211826013..211829699,5	K562	blood:
2	chr1:211824090..211825687-chr1:211827375..211829045,2	MCF-7	breast:
3	chr1:211743190..211745097-chr1:211827808..211829565,2	MCF-7	breast:
4	chr1:211750780..211752502-chr1:211827820..211829178,14	K562	blood:
5	chr1:211827406..211830383-chr1:211837337..211839241,2	MCF-7	breast:
6	chr1:211751216..211754175-chr1:211827530..211832882,6	K562	blood:
7	chr1:211432213..211433980-chr1:211827249..211829454,2	K562	blood:

Variant related genes	Relation type
ENSG00000222080	TF binding region
ENSG00000117625	Chromatin interaction
ENSG00000170385	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11119794	1.00[CHB][hapmap]
rs11578614	1.00[CHB][hapmap]
rs12074002	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12561861	1.00[CHB][hapmap]
rs12724388	1.00[JPT][hapmap]
rs12736496	1.00[JPT][hapmap]
rs12751701	1.00[JPT][hapmap]
rs17017716	1.00[CHB][hapmap]
rs2184844	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2794731	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs55661489	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56094815	0.92[ASN][1000 genomes]
rs6540695	1.00[JPT][hapmap]
rs6659316	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661565	1.00[CHB][hapmap]
rs6666442	1.00[JPT][hapmap]
rs6673372	1.00[JPT][hapmap]
rs701926	1.00[CHB][hapmap]
rs7511687	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7526473	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526891	1.00[CHB][hapmap]
rs7527002	1.00[CHB][hapmap]
rs7539988	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7551341	0.81[CEU][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs7553718	0.81[CEU][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs7554588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7516189	FAM71A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211811400-211829600	Enhancers	Fetal Intestine Small	intestine
2	chr1:211811600-211828200	Enhancers	Fetal Intestine Large	intestine
3	chr1:211817600-211830600	Weak transcription	Right Atrium	heart
4	chr1:211818400-211828400	Weak transcription	Adipose Nuclei	Adipose
5	chr1:211821800-211828400	Weak transcription	Colonic Mucosa	Colon
6	chr1:211822200-211828400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:211822800-211828200	Weak transcription	Liver	Liver
8	chr1:211822800-211828200	Weak transcription	Pancreas	Pancrea
9	chr1:211824000-211828200	Weak transcription	Stomach Mucosa	stomach
10	chr1:211825800-211828800	Enhancers	Placenta	Placenta
11	chr1:211826400-211828400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:211826400-211828600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:211826400-211828600	Flanking Active TSS	Hela-S3	cervix
14	chr1:211826800-211828200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:211826800-211828600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:211826800-211828600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:211826800-211828800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:211826800-211829600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:211827000-211828200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:211827000-211828400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:211827000-211828600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:211827000-211828600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:211827000-211828600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:211827000-211828600	Enhancers	HMEC	breast
25	chr1:211827000-211828600	Enhancers	NHDF-Ad	bronchial
26	chr1:211827000-211828800	Enhancers	NH-A	brain
27	chr1:211827000-211829000	Enhancers	K562	blood
28	chr1:211827000-211829200	Enhancers	A549	lung
29	chr1:211827400-211828200	Enhancers	Fetal Lung	lung
30	chr1:211827400-211828400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:211827400-211828600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:211827400-211828600	Enhancers	Fetal Heart	heart
33	chr1:211827400-211829000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:211827600-211828400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:211827600-211828600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:211827600-211828600	Bivalent Enhancer	Fetal Stomach	stomach
37	chr1:211827600-211828800	Enhancers	HUVEC	blood vessel
38	chr1:211827600-211833800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr1:211827600-211837600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:211827600-211847600	Weak transcription	HSMM	muscle
41	chr1:211827600-211847600	Weak transcription	NHEK	skin
42	chr1:211827800-211828200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:211827800-211828200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:211827800-211828200	Weak transcription	NHLF	lung
45	chr1:211827800-211828200	Weak transcription	Osteobl	bone
46	chr1:211827800-211828400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:211827800-211828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:211827800-211828400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:211827800-211828400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:211827800-211828400	Weak transcription	Rectal Mucosa Donor 31	rectum

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