Variant report

Variant	rs6698931
Chromosome Location	chr1:167015184-167015185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:167012456..167017091-chr1:167019887..167022128,4	K562	blood:

Variant related genes	Relation type
ENSG00000227907	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12126991	0.85[YRI][hapmap]
rs12133327	0.88[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs1410247	0.80[ASN][1000 genomes]
rs2025893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225153	0.98[ASN][1000 genomes]
rs3736988	0.88[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs393025	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4657621	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6427051	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6655947	0.85[YRI][hapmap]
rs6661553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6667210	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6673720	0.82[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs6693185	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs6694465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6696203	0.85[YRI][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	nsv1004148	chr1:166951869-167016311	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2750815	chr1:166953866-167180342	Enhancers Flanking Active TSS Strong transcription Weak 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	22 gene(s)	inside rSNPs	diseases
3	nsv519114	chr1:167003539-167015184	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6698931	RGS4	cis	cerebellum	SCAN
rs6698931	SDHC	cis	cerebellum	SCAN
rs6698931	UCK2	cis	cerebellum	SCAN
rs6698931	TADA1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:167013600-167022600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:167013800-167020600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:167013800-167021000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:167013800-167022600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:167013800-167028400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:167014000-167018400	Weak transcription	Primary T cells from cord blood	blood
7	chr1:167014000-167019000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:167014000-167019600	Weak transcription	Fetal Intestine Large	intestine
9	chr1:167014000-167020600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:167014000-167022600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:167014000-167028200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:167014200-167016800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:167014200-167019000	Weak transcription	Colonic Mucosa	Colon
14	chr1:167014200-167019600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:167014200-167021400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:167014200-167023000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:167014200-167025600	Weak transcription	Gastric	stomach
18	chr1:167014200-167028000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:167014400-167018200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:167015000-167023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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