Variant report

Variant	rs3846912
Chromosome Location	chr6:13657040-13657041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13656880..13659020-chr6:13704232..13705741,2	K562	blood:
2	chr6:13655854..13657836-chr6:13709414..13712393,2	K562	blood:
3	chr6:13656757..13659128-chr6:13659241..13662282,5	K562	blood:
4	chr6:13655040..13657479-chr6:13658664..13660741,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10484251	0.84[CHB][hapmap]
rs10807467	0.89[YRI][hapmap]
rs10948804	0.93[YRI][hapmap]
rs10948811	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11753232	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs11755634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11759518	0.84[CHB][hapmap]
rs11962124	0.89[YRI][hapmap]
rs11970591	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1362519	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1362520	0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1573702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071836	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2080415	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2237092	0.96[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2299026	0.82[CHB][hapmap]
rs2299027	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2841514	0.85[YRI][hapmap]
rs2841517	0.85[YRI][hapmap]
rs3757260	0.89[YRI][hapmap]
rs3800503	0.89[YRI][hapmap]
rs3906327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715455	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715512	0.84[CHB][hapmap]
rs59120082	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458997	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459003	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6459025	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6899402	0.93[YRI][hapmap]
rs6911121	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6915775	0.81[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940759	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72829117	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72831038	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741241	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7744218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475276	0.83[CHB][hapmap]

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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1016744	chr6:13622143-13664028	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1019422	chr6:13622143-13694781	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1026597	chr6:13634669-13689882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3846912	RANBP9	cis	cerebellum	SCAN
rs3846912	HIVEP1	cis	parietal	SCAN
rs3846912	CAP2	cis	parietal	SCAN
rs3846912	SIRT5	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13618200-13661200	Weak transcription	Fetal Brain Male	brain
2	chr6:13620400-13660400	Weak transcription	Pancreas	Pancrea
3	chr6:13620600-13691000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:13625400-13660400	Weak transcription	Gastric	stomach
5	chr6:13626000-13660400	Weak transcription	Lung	lung
6	chr6:13626600-13667800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:13626800-13669000	Weak transcription	Brain Anterior Caudate	brain
8	chr6:13632000-13660400	Weak transcription	Psoas Muscle	Psoas
9	chr6:13637400-13660400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:13638000-13661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:13638800-13657800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:13638800-13657800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:13638800-13659400	Weak transcription	Brain Angular Gyrus	brain
14	chr6:13639000-13660400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:13639000-13660600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:13639200-13658200	Weak transcription	Colonic Mucosa	Colon
17	chr6:13639200-13660400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:13639200-13662600	Weak transcription	Esophagus	oesophagus
19	chr6:13639400-13660400	Weak transcription	Ovary	ovary
20	chr6:13639400-13660600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:13639400-13662000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:13639400-13666000	Weak transcription	Fetal Brain Female	brain
23	chr6:13639400-13667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:13639600-13662600	Weak transcription	Aorta	Aorta
25	chr6:13639800-13660400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:13639800-13669800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:13640000-13660200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:13640000-13662600	Weak transcription	NHEK	skin
29	chr6:13640400-13662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:13643800-13664400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:13644000-13660400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:13644000-13663600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:13644200-13657800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:13644600-13659800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:13645200-13666800	Weak transcription	HMEC	breast
36	chr6:13648600-13657600	Strong transcription	Dnd41	blood
37	chr6:13650000-13657800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:13650000-13660000	Weak transcription	Fetal Lung	lung
39	chr6:13651200-13658600	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:13651400-13662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:13651600-13662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:13651800-13660400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:13652000-13658000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:13652400-13657400	Weak transcription	HSMMtube	muscle
45	chr6:13652400-13657600	Weak transcription	Primary T cells from cord blood	blood
46	chr6:13652400-13658400	Weak transcription	Placenta	Placenta
47	chr6:13652400-13658600	Weak transcription	Left Ventricle	heart
48	chr6:13652400-13660600	Weak transcription	Thymus	Thymus
49	chr6:13652400-13662600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:13652400-13662800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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