Variant report

Variant	rs13375836
Chromosome Location	chr1:161378897-161378898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161377159..161380003-chr1:161395367..161397564,2	MCF-7	breast:
2	chr1:161170434..161172328-chr1:161378596..161380361,2	K562	blood:
3	chr1:161372330..161375943-chr1:161377177..161380756,5	K562	blood:

Variant related genes	Relation type
ENSG00000215840	Chromatin interaction
ENSG00000158864	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13375736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376294	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16832949	0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs28742974	0.89[EUR][1000 genomes]
rs28874117	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4474277	0.82[CEU][hapmap]
rs55706531	0.85[EUR][1000 genomes]
rs55754455	0.85[EUR][1000 genomes]
rs55827435	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56295395	0.85[EUR][1000 genomes]
rs56871324	0.85[EUR][1000 genomes]
rs61734585	1.00[EUR][1000 genomes]
rs61998239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1010776	chr1:161282384-161409218	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv432998	chr1:161335902-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv872493	chr1:161339060-161413794	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv433009	chr1:161343927-161639328	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1005812	chr1:161343951-161548101	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv535182	chr1:161343951-161548101	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
10	nsv998957	chr1:161353351-161398414	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv433020	chr1:161355634-161673682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
12	esv2754329	chr1:161355728-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
13	nsv433031	chr1:161355728-161673682	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
14	nsv433042	chr1:161372038-161673682	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
15	nsv946461	chr1:161372505-161384947	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv3350498	chr1:161374323-161380643	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13375836	SDHC	Cis_1M	lymphoblastoid	RTeQTL
rs13375836	RP11-122G18.5	cis	Muscle Skeletal	GTEx
rs13375836	RP11-122G18.5	cis	Adipose Subcutaneous	GTEx
rs13375836	SDHC	cis	Whole Blood	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161370400-161379200	Weak transcription	Stomach Mucosa	stomach
2	chr1:161370400-161380000	Weak transcription	Gastric	stomach
3	chr1:161370600-161381800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:161370800-161379200	Weak transcription	Colonic Mucosa	Colon
5	chr1:161371000-161379000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:161371000-161379000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:161371000-161379000	Weak transcription	Right Atrium	heart
8	chr1:161371000-161379400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:161371000-161381400	Weak transcription	Esophagus	oesophagus
10	chr1:161371000-161387800	Weak transcription	Spleen	Spleen
11	chr1:161371200-161379000	Weak transcription	Psoas Muscle	Psoas
12	chr1:161371400-161379000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:161371600-161379000	Weak transcription	Right Ventricle	heart
14	chr1:161372200-161379800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:161374000-161379000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:161374200-161380000	Weak transcription	Small Intestine	intestine
17	chr1:161374800-161379800	Weak transcription	Fetal Lung	lung
18	chr1:161374800-161380000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:161377400-161381000	Enhancers	Fetal Intestine Large	intestine
20	chr1:161378000-161380000	Enhancers	K562	blood
21	chr1:161378200-161395400	Weak transcription	Pancreas	Pancrea
22	chr1:161378400-161379200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:161378600-161379000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr1:161378600-161379000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:161378600-161379200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr1:161378600-161379800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:161378600-161380200	Enhancers	HepG2	liver
28	chr1:161378800-161379400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr1:161378800-161379400	Enhancers	Fetal Intestine Small	intestine
30	chr1:161378800-161379400	Enhancers	Left Ventricle	heart
31	chr1:161378800-161379800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:161378800-161379800	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:161378800-161380000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:161378800-161380200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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