Variant report

Variant	rs12595074
Chromosome Location	chr15:57412016-57412017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57410833..57413680-chr15:57416630..57418139,2	K562	blood:
2	chr15:57209351..57211172-chr15:57411034..57413159,2	MCF-7	breast:
3	chr15:57411738..57417145-chr15:57421254..57425802,5	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1015967	0.85[JPT][hapmap]
rs10438332	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs11071307	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11071310	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11632502	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs11632526	1.00[YRI][hapmap]
rs11636655	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12324235	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12591367	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12593843	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1346880	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1625176	0.81[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs1631079	0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs1642936	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1642940	0.85[JPT][hapmap]
rs1652732	0.85[JPT][hapmap]
rs1652738	0.81[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs1652739	0.85[JPT][hapmap];0.86[MEX][hapmap]
rs1652740	0.85[JPT][hapmap]
rs1652741	0.85[JPT][hapmap]
rs17239222	1.00[YRI][hapmap]
rs17239459	0.81[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17819940	0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs17820018	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17820095	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1820996	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1867638	0.92[JPT][hapmap]
rs1870870	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2126402	1.00[YRI][hapmap]
rs213160	0.85[JPT][hapmap]
rs213163	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs213166	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs213168	0.85[JPT][hapmap]
rs2169468	1.00[YRI][hapmap]
rs2248620	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2252289	0.81[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2290939	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2431032	0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2435905	0.81[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs2439917	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2464427	0.81[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2464428	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2470080	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2470081	0.81[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2470083	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2470084	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2470085	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2566844	0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs2566856	0.81[GIH][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2585076	0.81[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs2585116	0.84[JPT][hapmap]
rs2591062	0.93[JPT][hapmap]
rs2591066	0.93[JPT][hapmap]
rs2593217	0.81[JPT][hapmap]
rs2593221	0.93[JPT][hapmap]
rs2593234	0.93[JPT][hapmap]
rs2593236	0.81[GIH][hapmap];0.93[JPT][hapmap]
rs2615228	0.92[JPT][hapmap]
rs2703588	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2703599	0.93[JPT][hapmap]
rs2703600	0.84[JPT][hapmap]
rs2733187	0.80[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2733309	0.92[JPT][hapmap]
rs2733318	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2733320	0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs2733330	0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs2920270	1.00[YRI][hapmap]
rs2920272	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2921430	0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2951900	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2951902	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2951907	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2957573	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2957576	0.81[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2957578	0.81[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2957592	1.00[YRI][hapmap]
rs2962988	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2962994	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2962995	1.00[YRI][hapmap]
rs3794617	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs55910715	0.84[EUR][1000 genomes]
rs6493909	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs7167268	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7182038	0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs7182188	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7183392	0.85[JPT][hapmap]
rs72751006	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72751008	0.84[AMR][1000 genomes]
rs72751021	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs734033	0.80[JPT][hapmap]
rs7359192	0.85[JPT][hapmap]
rs8023315	1.00[YRI][hapmap]
rs8024830	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs8029445	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs8035097	0.92[JPT][hapmap]
rs8037322	0.83[ASN][1000 genomes]
rs8037987	0.93[JPT][hapmap]
rs8042322	0.93[JPT][hapmap]
rs8043103	0.93[JPT][hapmap]
rs9806712	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12595074	UNC13C	cis	parietal	SCAN
rs12595074	ZNF280D	cis	parietal	SCAN
rs12595074	RSL24D1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
2	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57382800-57419600	Weak transcription	K562	blood
5	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
8	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
10	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
11	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
12	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
14	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
15	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:57404800-57415600	Weak transcription	Thymus	Thymus
19	chr15:57406800-57413000	Weak transcription	Gastric	stomach
20	chr15:57406800-57413000	Weak transcription	Left Ventricle	heart
21	chr15:57406800-57413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:57406800-57414200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr15:57406800-57414600	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:57406800-57416200	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
27	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
30	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
31	chr15:57407000-57413600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:57407400-57412600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr15:57407400-57413200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:57408200-57412800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr15:57408200-57413200	Weak transcription	Small Intestine	intestine
37	chr15:57408400-57414400	Weak transcription	Stomach Mucosa	stomach
38	chr15:57409200-57414000	Enhancers	Brain Substantia Nigra	brain
39	chr15:57409400-57412200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:57409400-57412600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:57409400-57415600	Enhancers	Brain Hippocampus Middle	brain
42	chr15:57409600-57412800	Enhancers	Brain Angular Gyrus	brain
43	chr15:57409800-57412200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr15:57409800-57412400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr15:57410000-57412600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr15:57410200-57412400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr15:57410200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr15:57410200-57415200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr15:57410400-57414600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:57410400-57425400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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