Variant report

Variant	rs1634814
Chromosome Location	chr12:120685747-120685748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
2	chr12:120684404..120691478-chr12:120697984..120705218,14	MCF-7	breast:
3	chr12:120685214..120692467-chr12:120727115..120732311,17	K562	blood:
4	chr12:120683364..120686301-chr12:120702145..120704591,2	K562	blood:
5	chr12:120685626..120692224-chr12:120727115..120732105,16	K562	blood:
6	chr12:120684888..120687057-chr12:120687063..120691406,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089159	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10744748	0.81[CHB][hapmap]
rs10849739	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11065035	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11065036	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11065061	1.00[CEU][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes]
rs11065064	0.96[EUR][1000 genomes]
rs1151824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1151825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1151827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151832	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151837	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182860	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11831552	0.98[EUR][1000 genomes]
rs1183781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12164847	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12305146	0.95[EUR][1000 genomes]
rs12308431	0.85[EUR][1000 genomes]
rs12310433	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12312562	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12321884	0.90[ASN][1000 genomes]
rs12581983	0.86[ASN][1000 genomes]
rs1634815	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2006194	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2074540	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2238155	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2238156	0.98[EUR][1000 genomes]
rs2238157	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2239208	1.00[CEU][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes]
rs2240312	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2240317	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2240318	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2240321	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2240322	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2240323	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2240325	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2269941	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2269944	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2269945	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2283362	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2283364	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2283365	0.99[EUR][1000 genomes]
rs2286049	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2286050	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2286051	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2524391	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3742039	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs3759397	0.98[EUR][1000 genomes]
rs3888586	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3888587	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs3888588	0.99[EUR][1000 genomes]
rs3890165	0.98[EUR][1000 genomes]
rs3956833	0.91[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs4767886	1.00[CEU][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes]
rs61198412	0.98[EUR][1000 genomes]
rs7134706	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7296380	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7300273	0.98[EUR][1000 genomes]
rs739809	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7953949	0.98[EUR][1000 genomes]
rs7966099	1.00[CEU][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1634814	HRK	cis	parietal	SCAN
rs1634814	PXN	cis	cerebellum	SCAN
rs1634814	FBXO21	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120665200-120692000	Enhancers	Placenta	Placenta
2	chr12:120666200-120686000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr12:120669800-120687600	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:120674200-120687600	Weak transcription	Fetal Kidney	kidney
5	chr12:120675800-120686400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:120676400-120687400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:120676400-120699400	Weak transcription	Aorta	Aorta
8	chr12:120676800-120685800	Weak transcription	Small Intestine	intestine
9	chr12:120678800-120687200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:120679600-120687200	Weak transcription	Brain Angular Gyrus	brain
11	chr12:120679800-120685800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:120679800-120686000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:120680000-120686000	Weak transcription	Colonic Mucosa	Colon
14	chr12:120680000-120687000	Weak transcription	Brain Anterior Caudate	brain
15	chr12:120680200-120687400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:120680400-120685800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:120680400-120687400	Weak transcription	Fetal Thymus	thymus
18	chr12:120681000-120686000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:120681000-120687200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:120682000-120689000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:120682600-120686400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:120682800-120687800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:120683000-120687200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:120683200-120685800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:120683200-120686000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:120683200-120686000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:120683200-120686000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:120683200-120686000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:120683200-120686000	Weak transcription	Brain Substantia Nigra	brain
30	chr12:120683200-120686000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:120683200-120686200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:120683200-120686200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:120683200-120687200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:120683200-120687200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:120683200-120687200	Weak transcription	Ovary	ovary
36	chr12:120683200-120687400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:120683200-120687400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:120683200-120687600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:120683200-120687600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:120683200-120694800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:120683200-120695200	Weak transcription	Fetal Brain Male	brain
42	chr12:120683400-120686000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:120683400-120686200	Weak transcription	Fetal Lung	lung
44	chr12:120683400-120686400	Weak transcription	Fetal Stomach	stomach
45	chr12:120683600-120686200	Enhancers	Psoas Muscle	Psoas
46	chr12:120684000-120685800	Enhancers	NHDF-Ad	bronchial
47	chr12:120684000-120692000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:120684600-120685800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:120684600-120687000	Enhancers	Fetal Muscle Leg	muscle
50	chr12:120684600-120687800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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