Variant report

Variant	rs12540595
Chromosome Location	chr7:3131792-3131793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10951052	0.84[ASN][1000 genomes]
rs12531881	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12537681	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12538887	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13438334	0.81[ASN][1000 genomes]
rs16870732	0.89[AFR][1000 genomes]
rs16870744	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17132968	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4445115	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs66883350	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9986825	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022938	chr7:2899514-3131881	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers 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	nsv605873	chr7:2920067-3204177	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1026476	chr7:2965034-3311344	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv538656	chr7:2965034-3311344	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv464260	chr7:2966138-3315572	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv605874	chr7:2966138-3315572	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1018287	chr7:2967524-3298539	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv538657	chr7:2967524-3298539	Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887319	chr7:3099853-3134593	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv887320	chr7:3110446-3134593	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv605875	chr7:3117801-3134593	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1020680	chr7:3125512-3204521	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1027945	chr7:3125512-3208071	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540595	KDELR2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3128800-3132200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr7:3128800-3134200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr7:3128800-3134400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:3129000-3131800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr7:3129000-3131800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr7:3129200-3131800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:3129400-3134200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:3129600-3132000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr7:3129600-3134600	Enhancers	Fetal Thymus	thymus
10	chr7:3130200-3134400	Enhancers	Primary B cells from peripheral blood	blood
11	chr7:3130200-3134400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:3130600-3133200	Enhancers	Primary hematopoietic stem cells	blood
13	chr7:3130600-3134200	Enhancers	Primary B cells from cord blood	blood
14	chr7:3130800-3131800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:3131000-3132000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr7:3131000-3132400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:3131000-3132600	Enhancers	Spleen	Spleen
18	chr7:3131000-3133200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr7:3131200-3131800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr7:3131200-3132200	Weak transcription	Thymus	Thymus
21	chr7:3131200-3134000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:3131200-3134400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:3131400-3131800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr7:3131400-3132000	Enhancers	Esophagus	oesophagus
25	chr7:3131400-3132200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr7:3131400-3132400	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr7:3131400-3132400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr7:3131600-3132000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:3131600-3132200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr7:3131600-3132400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr7:3131600-3132600	Enhancers	Dnd41	blood

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