Variant report

Variant	rs10829107
Chromosome Location	chr10:27135750-27135751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27134235..27137117-chr10:27142370..27144378,2	K562	blood:
2	chr10:27135138..27138155-chr10:27148362..27151068,3	K562	blood:
3	chr10:27135636..27137752-chr10:27138213..27139984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136754	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10159978	0.85[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10764642	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10764644	0.80[AFR][1000 genomes]
rs10764654	0.95[AFR][1000 genomes]
rs10829055	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829056	0.85[CEU][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829057	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829059	0.92[CEU][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10829061	0.92[CEU][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10829062	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10829068	0.92[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10829069	0.92[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10829072	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10829073	0.92[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10829074	0.85[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10829079	0.82[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10829083	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829085	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10829088	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829098	0.81[YRI][hapmap]
rs10829099	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs10829100	0.81[YRI][hapmap]
rs10829103	0.95[AFR][1000 genomes]
rs11015262	0.84[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015266	0.92[CEU][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap]
rs11015283	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11015298	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11015300	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11015308	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11015313	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11015333	0.80[YRI][hapmap]
rs11015336	0.80[YRI][hapmap]
rs11015340	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11015343	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12243481	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs12247684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12265625	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267091	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12358409	0.92[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1408530	0.92[CEU][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs16927341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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]
rs28538332	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7082503	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs718827	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10829107	HRG	trans	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27095000-27138600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr10:27095600-27148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:27111800-27147000	Weak transcription	Fetal Intestine Large	intestine
4	chr10:27119600-27147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:27120600-27142600	Weak transcription	HepG2	liver
6	chr10:27122600-27136800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:27122600-27143400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:27123000-27145000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:27124400-27146200	Weak transcription	Fetal Muscle Leg	muscle
10	chr10:27126600-27140000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:27127200-27137000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr10:27128000-27139600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:27128000-27143200	Weak transcription	Osteobl	bone
14	chr10:27128400-27136800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:27129200-27142600	Weak transcription	Right Ventricle	heart
16	chr10:27129400-27136200	Weak transcription	Left Ventricle	heart
17	chr10:27129400-27142000	Weak transcription	Lung	lung
18	chr10:27129400-27146000	Weak transcription	Pancreas	Pancrea
19	chr10:27129400-27146400	Weak transcription	Gastric	stomach
20	chr10:27129400-27146600	Weak transcription	Esophagus	oesophagus
21	chr10:27129400-27147200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:27129400-27148200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr10:27129600-27146600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:27130000-27140000	Weak transcription	Fetal Lung	lung
25	chr10:27130000-27143800	Weak transcription	Brain Angular Gyrus	brain
26	chr10:27130200-27140400	Weak transcription	Brain Anterior Caudate	brain
27	chr10:27130200-27143000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:27130200-27143600	Weak transcription	NHDF-Ad	bronchial
29	chr10:27130200-27145600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:27130800-27145000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:27131200-27140200	Weak transcription	Small Intestine	intestine
32	chr10:27131200-27143200	Weak transcription	Stomach Mucosa	stomach
33	chr10:27131200-27143400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr10:27131200-27146000	Weak transcription	Right Atrium	heart
35	chr10:27131600-27145000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr10:27132000-27142800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:27132400-27136200	Weak transcription	Fetal Intestine Small	intestine
38	chr10:27132600-27136000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr10:27132600-27136400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr10:27132600-27136800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr10:27132600-27137000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr10:27132800-27137000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:27132800-27137000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr10:27133000-27136600	Enhancers	Primary B cells from peripheral blood	blood
45	chr10:27133200-27140000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr10:27133600-27136400	Weak transcription	Ovary	ovary
47	chr10:27133600-27138200	Weak transcription	Colon Smooth Muscle	Colon
48	chr10:27133600-27146400	Weak transcription	Psoas Muscle	Psoas
49	chr10:27133600-27148200	Weak transcription	Aorta	Aorta
50	chr10:27133800-27136800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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