Variant report

Variant	rs12035190
Chromosome Location	chr1:227422862-227422863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227422402..227423241-chr1:227624998..227625702,5	MCF-7	breast:
2	chr1:227422234..227422915-chr1:227623464..227624323,2	MCF-7	breast:
3	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:
4	chr1:227422275..227423402-chr1:227625161..227626556,7	K562	blood:
5	chr1:227100019..227100963-chr1:227422287..227422908,3	MCF-7	breast:
6	chr1:227422445..227422950-chr1:227635271..227635835,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADCK3-6	chr1:227422753-227423056	NONHSAT009917

No data

Variant related genes	Relation type
ENSG00000242757	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10799411	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10916098	0.83[AMR][1000 genomes]
rs10916110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916117	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12033050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12038272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[ASN][1000 genomes]
rs12073573	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12079122	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12079173	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080452	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12095674	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12097121	0.83[AMR][1000 genomes]
rs16847690	0.82[ASW][hapmap]
rs4065211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653828	0.90[ASW][hapmap]
rs533134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs61700597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834325	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834563	0.89[EUR][1000 genomes]
rs61834564	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs645081	0.83[AMR][1000 genomes]
rs6660043	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6664803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6699534	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs688718	0.83[AMR][1000 genomes]
rs72757311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513122	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12035190	PARP1	cis	cerebellum	SCAN
rs12035190	MIXL1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
4	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
5	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
6	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227414000-227424400	Weak transcription	Psoas Muscle	Psoas
8	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227414200-227423400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:227414200-227424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227414200-227424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:227414200-227453800	Weak transcription	HSMM	muscle
16	chr1:227414400-227423000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:227414400-227423000	Weak transcription	Brain Substantia Nigra	brain
18	chr1:227414400-227423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:227415400-227424400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
25	chr1:227421800-227423000	Enhancers	Left Ventricle	heart
26	chr1:227422000-227430800	Weak transcription	Ovary	ovary
27	chr1:227422200-227423600	Enhancers	Brain Anterior Caudate	brain
28	chr1:227422200-227423600	Enhancers	Brain Hippocampus Middle	brain
29	chr1:227422200-227423800	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:227422200-227424000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:227422400-227423000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:227422400-227424000	Enhancers	K562	blood
33	chr1:227422600-227423200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:227422600-227430800	Weak transcription	Gastric	stomach
35	chr1:227422800-227423000	Enhancers	Small Intestine	intestine
36	chr1:227422800-227423200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:227422800-227423200	Enhancers	A549	lung
38	chr1:227422800-227423400	Enhancers	HUVEC	blood vessel
39	chr1:227422800-227423600	Enhancers	Liver	Liver
40	chr1:227422800-227423600	Enhancers	Colon Smooth Muscle	Colon

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